Filters¶

Here is the list of filters available to limit the variants, genotypes or samples taken into account.

Position Filters¶

keep-pos¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep Variants starting on a comma-separated list of positions.</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-pos chr[:start[-end]],...

Examples
--keep-pos 14 : All variants from chromosome 14
--keep-pos chr12 : All variants from chromosome 12
--keep-pos 10:145678 : All variants at position 10:145678
--keep-pos chr3:10000-20000 : All variants in region 10000-20000 on chromosome 3
--keep-pos chr3:10000-20000,chr3:30000-40000,chr3:50000-60000 : All variants in regions 10000-20000, 30000-40000 or 50000-60000 on chromosome 3

keep-positions¶

Keep Variants starting on positions listed in a file.

Lines in the position file can have the following format

chr #comment
chr:pos #comment
chr:start-end #comment
chr[tab]pos #comment
chr[tab]start[tab]end #comment

Syntax :

--keep-positions filename.txt

Example

--keep-positions my_positions.txt : All positions listed in my_positions.txt

keep-bed¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep Variants starting on regions defined by a bed file. See FileFormats</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-bed filename.bed

Example

--keep-bed my_regions.bed : All regions defined in the bed file my_regions.bed

keep-pos-overlap¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep Variants overlapping on a comma-separated list of positions.</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-pos-overlap chr[:start[-end]],...

Examples
--keep-pos-overlap 14 : All variants from chromosome 14
--keep-pos-overlap chr12 : All variants from chromosome 12
--keep-pos-overlap 10:145678 : All variants at position 10:145678
--keep-pos-overlap chr3:10000-20000 : All variants in region 10000-20000 on chromosome 3
--keep-pos-overlap chr3:10000-20000,chr3:30000-40000,chr3:50000-60000 : All variants in regions 10000-20000, 30000-40000 or 50000-60000 on chromosome 3

keep-positions-overlap¶

Keep Variants overlapping positions listed in a file.

Lines in the position file can have the following format

chr #comment
chr:pos #comment
chr:start-end #comment
chr[tab]pos #comment
chr[tab]start[tab]end #comment

Syntax :

--keep-positions-overlap filename.txt

Example

--keep-positions-overlap my_positions.txt : All positions listed in my_positions.txt

remove-pos¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove Variants starting on a comma-separated list of positions.</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-pos chr[:start[-end]],...

Examples
--remove-pos 14 : All variants from chromosome 14
--remove-pos chr12 : All variants from chromosome 12
--remove-pos 10:145678 : All variants at position 10:145678
--remove-pos chr3:10000-20000 : All variants in region 10000-20000 on chromosome 3
--remove-pos chr3:10000-20000,chr3:30000-40000,chr3:50000-60000 : All variants in regions 10000-20000, 30000-40000 or 50000-60000 on chromosome 3

remove-positions¶

Remove Variants starting on positions listed in a file.

Lines in the position file can have the following format

chr #comment
chr:pos #comment
chr:start-end #comment
chr[tab]pos #comment
chr[tab]start[tab]end #comment

Syntax :

--remove-positions filename.txt

Example

--remove-positions my_positions.txt : All positions listed in my_positions.txt

remove-bed¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep Variants starting on regions defined by a bed file. See FileFormats</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-bed filename.bed

Example

--remove-bed my_regions.bed : All regions defined in the bed file my_regions.bed

remove-pos-overlap¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove Variants overlapping a comma-separated list of positions.</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-pos-overlap chr[:start[-end]],...

Examples
--remove-pos-overlap 14 : All variants from chromosome 14
--remove-pos-overlap chr12 : All variants from chromosome 12
--remove-pos-overlap 10:145678 : All variants at position 10:145678
--remove-pos-overlap chr3:10000-20000 : All variants in region 10000-20000 on chromosome 3
--remove-pos-overlap chr3:10000-20000,chr3:30000-40000,chr3:50000-60000 : All variants in regions 10000-20000, 30000-40000 or 50000-60000 on chromosome 3

remove-positions-overlap¶

Remove Variants overlapping positions listed in a file.

Lines in the position file can have the following format

chr #comment
chr:pos #comment
chr:start-end #comment
chr[tab]pos #comment
chr[tab]start[tab]end #comment

Syntax :

--remove-positions-overlap filename.txt

Example

--remove-positions-overlap my_positions.txt : All positions listed in my_positions.txt

thin¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Thin sites so that no two sites are within the specified distance from one another.</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--thin distance (integer no_units, kb or mb)

Examples
--thin 1000 : avoids having sites closer than 1kb from each other
--thin 1kb : avoids having sites closer than 1kb from each other
--thin 5000000 : avoids having sites closer than 5mb from each other
--thin 5mb : avoids having sites closer than 5mb from each other

Sample Filters¶

keep-sample¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only the samples given in a comma-separated list</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-sample Sample1,Sample2,...

Example

--keep-sample Charlie,Juliett,Mike,Romeo,Victor : Only the samples Charlie, Juliett, Mike, Romeo and Victor are kept

remove-sample¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove the samples given in a comma-separated list</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-sample Sample1,Sample2,...

Example

--remove-sample Charlie,Juliett,Mike,Romeo,Victor : The samples Charlie, Juliett, Mike, Romeo and Victor are removed

keep-samples¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only the sample listed in the given file (one per line)</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-samples filename.txt

Example

--keep-samples samples.list.txt : Keep only the sample listed in samples.list.txt (one per line)

remove-samples¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove the sample listed in the given file (one per line)</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-samples filename.txt

Example

--remove-samples samples.list.txt : Remove the sample listed in samples.list.txt (one per line)

max-sample¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove random samples to keep only the provided number of samples</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-sample number-of-samples (integer)

Example

--max-sample 5 : Keep only 5 samples at random

ped¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only the samples described in the given PED file (see file formats)</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--ped filename.ped

Example

--ped cohort.ped : Keep only the samples described in cohort.ped

keep-family¶

Keep only the sample with given FamilyID

Warning

has to be combined to --ped

Syntax :

--keep-family Fam1,Fam2,...

Example

--keep-family Fam1,Fam2 : Keep only the samples whose FamilyID are Fam1 or Fam2

remove-family¶

Remove the sample with given FamilyID

Warning

has to be combined to --ped

Syntax :

--remove-family Fam1,Fam2,...

Example

--remove-family Fam1,Fam2 : Remove the samples whose FamilyID are Fam1 or Fam2

keep-sex¶

Keep only the sample with given sex

Warning

has to be combined to --ped

Syntax :

--keep-sex sex (integer)

Example

--keep-sex 1 : Keep only the samples whose sex are 1

remove-sex¶

Remove the sample with given sex

Warning

has to be combined to --ped

Syntax :

--remove-sex sex (integer)

Example

--remove-sex 1 : Remove the samples whose sex are 1

keep-phenotype¶

Keep only the sample with given phenotype

Warning

has to be combined to --ped

Syntax :

--keep-phenotype phenotype (integer)

Example

--keep-phenotype 1 : Keep only the samples whose phenotype are 1

remove-phenotype¶

Remove the sample with given phenotype

Warning

has to be combined to --ped

Syntax :

--remove-phenotype phenotype (integer)

Example

--remove-phenotype 1 : Remove the samples whose phenotype are 1

keep-group¶

Keep only the sample belonging to given phenotype

Warning

has to be combined to --ped

Syntax :

--keep-group Group1,Group2,...

Example

--keep-group CohortA,CohortB : Keep only the samples belonging to CohortA or CohortB

remove-group¶

Remove the sample belonging to given phenotype

Warning

has to be combined to --ped

Syntax :

--remove-group Group1,Group2,...

Example

--remove-group CohortA,CohortB : Remove the samples belonging to CohortA or CohortB

Genotype Filters¶

remove-filtered-geno-all¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing when the FT field has any value besides “.” or “PASS”</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-filtered-geno-all

keep-filtered-geno¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing when the FT field doesn’t have at least one of the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-filtered-geno Tag1,Tag2,...

Example

--keep-filtered-geno Tag1,Tag2 : Sets genotypes to missing when the FT field doesn’t have the value Tag1 and/or Tag2

remove-filtered-geno¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing when the FT field has at least one of the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-filtered-geno Tag1,Tag2,...

Example

--remove-filtered-geno Tag1,Tag2 : Sets genotypes to missing when the FT field has the value Tag1 and/or Tag2

minDP¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing if DP is below the given value (or SUM(AD) if DP is missing)</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--minDP depth-of-coverage (integer)

Example

--minDP 10 : Sets genotypes to missing if DP <10 (or SUM(AD) if DP is missing)

maxDP¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing if DP is above the given value (or SUM(AD) if DP is missing)</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--maxDP depth-of-coverage (integer)

Example

--maxDP 10 : Sets genotypes to missing if DP >10 (or SUM(AD) if DP is missing)

minGQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing if GQ is below the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--minGQ Genotype Quality (integer)

Example

--minGQ 30 : Sets genotypes to missing if GQ <30

maxGQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Sets genotypes to missing if GQ is above the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--maxGQ Genotype Quality (integer)

Example

--maxGQ 30 : Sets genotypes to missing if GQ >30

Variant Frequency Filters¶

min-maf¶

Keep only variants with AF of the rarest reference/alternate allele above the threshold

Warning

Diploid variants expected

Syntax :

--min-maf frequency (double)

Example

--min-maf 0.05 : Keep only variants with AF of the rarest reference/alternate allele above 5%

max-maf¶

Keep only variants with AF of the rarest reference/alternate allele below the threshold

Warning

Diploid variants expected

Syntax :

--max-maf frequency (double)

Example

--max-maf 0.05 : Keep only variants with AF of the rarest reference/alternate allele below 5%

min-group-maf¶

Keep only variants with AF of the rarest reference/alternate allele above the threshold in every group

Warning

has to be combined to --ped

Warning

Diploid variants expected

Syntax :

--min-group-maf frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--min-group-maf GRP1:0.05,GRP2:0.07 : Keep only variants with AF of the rarest reference/alternate allele above 5% in GRP1 and 7% in GRP2

max-group-maf¶

Keep only variants with AF of the rarest reference/alternate allele below the threshold in every group

Warning

has to be combined to --ped

Warning

Diploid variants expected

Syntax :

--max-group-maf frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--max-group-maf GRP1:0.05,GRP2:0.07 : Keep only variants with AF of the rarest reference/alternate allele below 5% in GRP1 and 7% in GRP2

min-ref-af¶

Keep only variants with AF of the reference allele above the threshold

Warning

Diploid variants expected

Syntax :

--min-ref-af frequency (double)

Example

--min-ref-af 0.05 : Keep only variants with AF of the reference allele above 5%

max-ref-af¶

Keep only variants with AF of the reference allele below the threshold

Warning

Diploid variants expected

Syntax :

--max-ref-af frequency (double)

Example

--max-ref-af 0.05 : Keep only variants with AF of the reference allele below 5%

min-group-ref-af¶

Keep only variants with AF of the reference allele above the threshold in every group

Warning

has to be combined to --ped

Warning

Diploid variants expected

Syntax :

--min-group-ref-af frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--min-group-ref-af GRP1:0.05,GRP2:0.07 : Keep only variants with AF of the reference allele above 5% in GRP1 and 7% in GRP2

max-group-ref-af¶

Keep only variants with AF of the reference allele below the threshold in every group

Warning

has to be combined to --ped

Warning

Diploid variants expected

Syntax :

--max-group-ref-af frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--max-group-ref-af GRP1:0.05,GRP2:0.07 : Keep only variants with AF of the reference allele below 5% in GRP1 and 7% in GRP2

min-all-non-ref-af¶

Keep only variants with AF of all the alternate allele above the threshold

Warning

Diploid variants expected

Syntax :

--min-all-non-ref-af frequency (double)

Example

--min-all-non-ref-af 0.05 : Keep only variants with AF of all the alternate allele above 5%

max-all-non-ref-af¶

Keep only variants with AF of all the alternate allele below the threshold

Warning

Diploid variants expected

Syntax :

--max-all-non-ref-af frequency (double)

Example

--max-all-non-ref-af 0.05 : Keep only variants with AF of all the alternate allele below 5%

min-group-all-non-ref-af¶

Keep only variants with AF of all the alternate allele above the threshold in every group

Warning

has to be combined to --ped

Warning

Diploid variants expected

Syntax :

--min-group-all-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--min-group-all-non-ref-af GRP1:0.05,GRP2:0.07 : Keep only variants with AF of all the alternate allele above 5% in GRP1 and 7% in GRP2

max-group-all-non-ref-af¶

Keep only variants with AF of all the alternate allele below the threshold in every group

Warning

has to be combined to --ped

Warning

Diploid variants expected

Syntax :

--max-group-all-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--max-group-all-non-ref-af GRP1:0.05,GRP2:0.07 : Keep only variants with AF of all the alternate allele below 5% in GRP1 and 7% in GRP2

min-any-non-ref-af¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AF of any alternate allele above the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-any-non-ref-af frequency (double)

Example

--min-any-non-ref-af 0.05 : Keep only variants with AF of any alternate allele above 5%

max-any-non-ref-af¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AF of any alternate allele below the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-any-non-ref-af frequency (double)

Example

--max-any-non-ref-af 0.05 : Keep only variants with AF of any alternate allele below 5%

min-group-any-non-ref-af¶

Keep only variants with AF of any alternate allele above the threshold in every group

Warning

has to be combined to --ped

Syntax :

--min-group-any-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--min-group-any-non-ref-af GRP1:0.05,GRP2:0.07 : Keep only variants with AF of any alternate allele above 5% in GRP1 and 7% in GRP2

max-group-any-non-ref-af¶

Keep only variants with AF of any alternate allele below the threshold in every group

Warning

has to be combined to --ped

Syntax :

--max-group-any-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN)

Example

--max-group-any-non-ref-af GRP1:0.05,GRP2:0.07 : Keep only variants with AF of any alternate allele below 5% in GRP1 and 7% in GRP2

min-ref-ac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of the reference allele above the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-ref-ac allele-count (integer)

Example

--min-ref-ac 12 : Keep only variants with AC of the reference allele above 12

max-ref-ac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of the reference allele below the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-ref-ac allele-count (integer)

Example

--max-ref-ac 12 : Keep only variants with AC of the reference allele below 12

min-group-ref-ac¶

Keep only variants with AC of the reference allele above the threshold in every group

Warning

has to be combined to --ped

Syntax :

--min-group-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--min-group-ref-ac GRP1:8,GRP2:6 : Keep only variants with AC of the reference allele above 8 in GRP1 and 6 in GRP2

max-group-ref-ac¶

Keep only variants with AC of the reference allele below the threshold in every group

Warning

has to be combined to --ped

Syntax :

--max-group-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--max-group-ref-ac GRP1:8,GRP2:6 : Keep only variants with AC of the reference allele below 8 in GRP1 and 6 in GRP2

min-all-non-ref-ac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of all the alternate allele above the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-all-non-ref-ac allele-count (integer)

Example

--min-all-non-ref-ac 12 : Keep only variants with AC of all the alternate allele above 12

max-all-non-ref-ac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of all the alternate allele below the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-all-non-ref-ac allele-count (integer)

Example

--max-all-non-ref-ac 12 : Keep only variants with AC of all the alternate allele below 12

min-group-all-non-ref-ac¶

Keep only variants with AC of all the alternate allele above the threshold in every group

Warning

has to be combined to --ped

Syntax :

--min-group-all-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--min-group-all-non-ref-ac GRP1:8,GRP2:6 : Keep only variants with AC of all the alternate allele above 8 in GRP1 and 6 in GRP2

max-group-all-non-ref-ac¶

Keep only variants with AC of all the alternate allele below the threshold in every group

Warning

has to be combined to --ped

Syntax :

--max-group-all-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--max-group-all-non-ref-ac GRP1:8,GRP2:6 : Keep only variants with AC of all the alternate allele below 8 in GRP1 and 6 in GRP2

min-mac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of the rarest alternate reference/allele above the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-mac allele-count (integer)

Example

--min-mac 12 : Keep only variants with AC of the rarest reference/alternate allele above 12

max-mac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of the rarest reference/alternate allele below the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-mac allele-count (integer)

Example

--max-mac 12 : Keep only variants with AC of the rarest reference/alternate allele below 12

min-group-mac¶

Keep only variants with AC of the rarest reference/alternate allele above the threshold in every group

Warning

has to be combined to --ped

Syntax :

--min-group-mac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--min-group-mac GRP1:8,GRP2:6 : Keep only variants with AC of the rarest reference/alternate allele above 8 in GRP1 and 6 in GRP2

max-group-mac¶

Keep only variants with AC of the rarest reference/alternate allele below the threshold in every group

Warning

has to be combined to --ped

Syntax :

--max-group-mac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--max-group-mac GRP1:8,GRP2:6 : Keep only variants with AC of the rarest reference/alternate allele below 8 in GRP1 and 6 in GRP2

min-any-non-ref-ac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of any alternate allele above the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-any-non-ref-ac allele-count (integer)

Example

--min-any-non-ref-ac 12 : Keep only variants with AC of any alternate allele above 12

max-any-non-ref-ac¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep only variants with AC of any alternate allele below the threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-any-non-ref-ac allele-count (integer)

Example

--max-any-non-ref-ac 12 : Keep only variants with AC of any alternate allele below 12

min-group-any-non-ref-ac¶

Keep only variants with AC of any alternate allele above the threshold in every group

Warning

has to be combined to --ped

Syntax :

--min-group-any-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--min-group-any-non-ref-ac GRP1:8,GRP2:6 : Keep only variants with AC of any alternate allele above 8 in GRP1 and 6 in GRP2

max-group-any-non-ref-ac¶

Keep only variants with AC of any alternate allele below the threshold in every group

Warning

has to be combined to --ped

Syntax :

--max-group-any-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN)

Example

--max-group-any-non-ref-ac GRP1:8,GRP2:6 : Keep only variants with AC of any alternate allele below 8 in GRP1 and 6 in GRP2

Variant Property Filters¶

keep-id¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep Variants with ID field matching a comma-separated list of ID (e.g. a dbSNP rsID).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-id id1,id2,....

Examples
--keep-id rs123456 : variants with ID matching rs123456
--keep-id rs123456,COSM654321 : variants with ID matching rs123456 or COSM654321

remove-id¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove Variants with ID field matching a comma-separated list of ID (e.g. a dbSNP rsID).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-id id1,id2,....

Examples
--remove-id rs123456 : variants with ID matching rs123456
--remove-id rs123456,COSM654321 : variants with ID matching rs123456 or COSM654321

keep-ids¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep Variants with ID matching the ones listed in the file (one per line).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-ids filename.txt

Example

--keep-ids selected.id.txt : variants with ID list in the file selected.id.txt

remove-ids¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove Variants with ID matching the ones listed in the file (one per line).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-ids filename.txt

Example

--remove-ids selected.id.txt : variants with ID list in the file selected.id.txt

keep-indels¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant sites where at least one alternate allele is an indel (AC->GT is considered as an SNV not an INDEL).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-indels

remove-indels¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove variant sites where at least one alternate allele is an indel (AC->GT is considered as an SNV not an INDEL).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-indels

keep-snvs¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant sites where at least one alternate allele is an SNV (AC->GT is considered as an SNV not an INDEL).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-snvs

remove-snvs¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove variant sites where at least one alternate allele is an SNV (AC->GT is considered as an SNV not an INDEL).</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-snvs

keep-filtered-all¶

to pass, all variant’s Tags must be listed

sites removed by --remove-filtered-all are kept

A,B

keepall

keepany

removeall

removeany

keepstrictall

keepstrictany

removestrictall

removestrictany

A

pass

pass

filtered

filtered

filtered

filtered

pass

pass

B

pass

pass

filtered

filtered

filtered

filtered

pass

pass

C

filtered

filtered

pass

pass

filtered

filtered

pass

pass

A;B

pass

pass

filtered

filtered

pass

pass

filtered

filtered

A;C

filtered

pass

pass

filtered

filtered

filtered

pass

pass

B;C

filtered

pass

pass

filtered

filtered

filtered

pass

pass

A;B;C

filtered

pass

pass

filtered

filtered

pass

pass

filtered

Syntax :

--keep-filtered-all Tag1,Tag2,...

Example

--keep-filtered-all Tag1,Tag2 : Variants with Tag1 and/or Tag2 and no other will be kept

keep-filtered-any¶

to pass, any variant’s Tag must be listed (plus any other)
sites removed by --remove-filtered-any are kept

Syntax :

--keep-filtered-any Tag1,Tag2,...

Example

--keep-filtered-any Tag1,Tag2 : Variants with Tag1 and/or Tag2 (plus any other) will be kept

remove-filtered-all¶

to pass, any of the variant’s Tags must not be listed
sites kept by --keep-filtered-all are removed

Syntax :

--remove-filtered-all Tag1,Tag2,...

Example

--remove-filtered-all Tag1,Tag2 : Variants with Tag1 and/or Tag2 and no other will be removed

remove-filtered-any¶

to pass, none of the variant’s Tags must be listed
sites kept by --keep-filtered-any are removed

Syntax :

--remove-filtered-any Tag1,Tag2,...

Example

--remove-filtered-any Tag1,Tag2 : Variants with Tag1 and/or Tag2 (and any other) will be removed

strict-keep-filtered-all¶

to pass, the variant must have all listed Tags, and no other
sites removed by --strict-remove-filtered-all are kept

Syntax :

--strict-keep-filtered-all Tag1,Tag2,...

Example

--strict-keep-filtered-all Tag1,Tag2 : Variants with Tag1 and/or Tag2 and no other will be kept

strict-keep-filtered-any¶

to pass, the variant must have all listed Tags (plus any other)
sites removed by --strict-remove-filtered-any are kept

Syntax :

--strict-keep-filtered-any Tag1,Tag2,...

Example

--strict-keep-filtered-any Tag1,Tag2 : Variants with Tag1 and Tag2 (plus any other) will be kept

strict-remove-filtered-all¶

to pass, the variant must not have all the listed Tags, and no other
sites kept by --strict-keep-filtered-all are removed

Syntax :

--strict-remove-filtered-all Tag1,Tag2,...

Example

--strict-remove-filtered-all Tag1,Tag2 : Variants with Tag1 and Tag2, and not other will be removed

strict-remove-filtered-any¶

to pass, the variant must not have all the listed Tags (plus any other)
sites kept by --strict-keep-filtered-all are removed

Syntax :

--strict-remove-filtered-any Tag1,Tag2,...

Example

--strict-remove-filtered-any Tag1,Tag2 : Variants with Tag1 and Tag2 (plus any other tag) will be removed

keep-any-info¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Variant with any of the listed Info Fields are kept</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-any-info Info1,Info2,...

Example

--keep-any-info Info1,Info2 : Variant with Info1 and/or Info2 field in the INFO column are kept

keep-all-info¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Variant with all the listed Info Fields are kept</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--keep-all-info Info1,Info2,...

Example

--keep-all-info Info1,Info2 : Variant with Info1 and Info2 field in the INFO column are kept

remove-any-info¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Variant with any of the listed Info Fields are removed</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-any-info Info1,Info2,...

Example

--remove-any-info Info1,Info2 : Variant with Info1 and/or Info2 field in the INFO column are removed

remove-all-info¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Variant with all the listed Info Fields are removed</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-all-info Info1,Info2,...

Example

--remove-all-info Info1,Info2 : Variant with Info1 and Info2 field in the INFO column are removed

min-alleles¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with at least the number of specified alleles (reference plus alternates</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-alleles number of alleles

Example

--min-alleles 3 : Keep variants with at least 3 alleles (1 reference and 2 alternates)

max-alleles¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with at most the number of specified alleles (reference plus alternates</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-alleles number of alleles

Example

--max-alleles 3 : Keep variants with at most 3 alleles (1 reference and 2 alternates)

min-meanDP¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a mean Depth of coverage accross samples at least equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-meanDP depth-of-coverage (integer)

Example

--min-meanDP 10 : Keep variants with a mean DP accross samples at least equal to 10

min-medianDP¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a median Depth of coverage accross samples at least equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-medianDP depth-of-coverage (integer)

Example

--min-medianDP 10 : Keep variants with a median DP accross samples at least equal to 10

max-meanDP¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a mean Depth of coverage accross samples at most equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-meanDP depth-of-coverage (integer)

Example

--max-meanDP 10 : Keep variants with a mean DP accross samples at most equal to 10

max-medianDP¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a median Depth of coverage accross samples at most equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-medianDP depth-of-coverage (integer)

Example

--max-medianDP 10 : Keep variants with a median DP accross samples at most equal to 10

min-meanGQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a mean Genotype Quality accross samples at least equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-meanGQ genotype-quality (integer)

Example

--min-meanGQ 10 : Keep variants with a mean GQ accross samples at least equal to 10

min-medianGQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a median Genotype Quality accross samples at least equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-medianGQ genotype-quality (integer)

Example

--min-medianGQ 10 : Keep variants with a median GQ accross samples at least equal to 10

max-meanGQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a mean Genotype Quality accross samples at most equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-meanGQ genotype-quality (integer)

Example

--max-meanGQ 10 : Keep variants with a mean GQ accross samples at most equal to 10

max-medianGQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a median Genotype Quality accross samples at most equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-medianGQ genotype-quality (integer)

Example

--max-medianGQ 10 : Keep variants with a median GQ accross samples at most equal to 10

hwe¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with Hardy-Weinberg Equilibrium p-value above the given threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--hwe p-value (double)

Example

--hwe 0.0000001 : Keep variants with HWE p-value >= 0.0000001

remove-hwe¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove variants with Hardy-Weinberg Equilibrium p-value above the given threshold</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-hwe p-value (double)

Example

--remove-hwe 0.0000001 : Remove variants with HWE p-value >= 0.0000001

max-missing¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant with at most the given ratio of missing genotypes</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-missing ratio (double)

Example

--max-missing 0.1 : Keep variant with less than 10% of missing genotypes

min-missing¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant with at least the given ratio of missing genotypes</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-missing ratio (double)

Example

--min-missing 0.1 : Keep variant with more than 10% of missing genotypes

max-missing-count¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant with at most the given number of missing genotypes</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--max-missing-count integer

Example

--max-missing-count 17 : Keep variant with less than 17 missing genotypes

min-missing-count¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant with at least the given number of missing genotypes</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--min-missing-count integer

Example

--min-missing-count 17 : Keep variant with more than 17 missing genotypes

phased¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variant without unphased genotypes</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--phased

remove-phased¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Remove variant without unphased genotypes</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--remove-phased

minQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a quality (VCF column QUALITY) at least equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--minQ quality (double)

Example

--minQ 500 : Keep variants with QUALITY >= 500

maxQ¶

<table border=”1” class=”docutils”> <thead> <tr> <th>Keep variants with a quality (VCF column QUALITY) at most equal to the given value</th> </tr> </thead> <tbody> <tr> <td><strong>Syntax :</strong></td> </tr> </tbody> </table>

--maxQ quality (double)

Example

--maxQ 500 : Keep variants with QUALITY <= 500