Filters

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

Position Filters

keep-pos

Keep Variants starting on a comma-separated list of positions.

Syntax :

--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

Keep Variants starting on regions defined by a bed file. See FileFormats

Syntax :

--keep-bed filename.bed

Example

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

keep-pos-overlap

Keep Variants overlapping on a comma-separated list of positions.

Syntax :

--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

Remove Variants starting on a comma-separated list of positions.

Syntax :

--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

Keep Variants starting on regions defined by a bed file. See FileFormats

Syntax :

--remove-bed filename.bed

Example

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

remove-pos-overlap

Remove Variants overlapping a comma-separated list of positions.

Syntax :

--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

Thin sites so that no two sites are within the specified distance from one another.

Syntax :

--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

Keep only the samples given in a comma-separated list

Syntax :

--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

Remove the samples given in a comma-separated list

Syntax :

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

Example

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

keep-samples

Keep only the sample listed in the given file (one per line)

Syntax :

--keep-samples filename.txt

Example

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

remove-samples

Remove the sample listed in the given file (one per line)

Syntax :

--remove-samples filename.txt

Example

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

max-sample

Remove random samples to keep only the provided number of samples

Syntax :

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

Example

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

ped

Keep only the samples described in the given PED file (see file formats)

Syntax :

--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

Sets genotypes to missing when the FT field has any value besides “.” or “PASS”

Syntax :

--remove-filtered-geno-all

keep-filtered-geno

Sets genotypes to missing when the FT field doesn’t have at least one of the given value

Syntax :

--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

Sets genotypes to missing when the FT field has at least one of the given value

Syntax :

--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

Sets genotypes to missing if DP is below the given value (or SUM(AD) if DP is missing)

Syntax :

--minDP depth-of-coverage (integer)

Example

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

maxDP

Sets genotypes to missing if DP is above the given value (or SUM(AD) if DP is missing)

Syntax :

--maxDP depth-of-coverage (integer)

Example

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

minGQ

Sets genotypes to missing if GQ is below the given value

Syntax :

--minGQ Genotype Quality (integer)

Example

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

maxGQ

Sets genotypes to missing if GQ is above the given value

Syntax :

--maxGQ Genotype Quality (integer)

Example

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

minVAF

Sets genotypes to missing if VAF is below the given value

Syntax :

--minVAF VAF = AD(variant)/DP

Example

--minVAF .35 : Sets genotypes to missing if VAR <.35

maxVAF

Sets genotypes to missing if VAF is above the given value

Syntax :

--maxVAF VAF = AD(variant)/DP

Example

--maxVAF .7 : Sets genotypes to missing if VAR > .7

abhetdev

Sets genotypes to missing if AB < 0.5-deviation or AB > 0.5+deviation

Syntax :

--abhetdev AB = AD1 / (AD1+AD2)

Example

--abhetdev 0.25 : Sets genotypes to missing if AB < 0.25-deviation or AB > 0.75

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

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

Syntax :

--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

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

Syntax :

--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

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

Syntax :

--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

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

Syntax :

--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

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

Syntax :

--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

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

Syntax :

--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

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

Syntax :

--min-mac allele-count (integer)

Example

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

max-mac

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

Syntax :

--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

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

Syntax :

--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

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

Syntax :

--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

Keep Variants with ID field matching a comma-separated list of ID (e.g. a dbSNP rsID).

Syntax :

--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

Remove Variants with ID field matching a comma-separated list of ID (e.g. a dbSNP rsID).

Syntax :

--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

Keep Variants with ID matching the ones listed in the file (one per line).

Syntax :

--keep-ids filename.txt

Example

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

remove-ids

Remove Variants with ID matching the ones listed in the file (one per line).

Syntax :

--remove-ids filename.txt

Example

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

keep-indels

Keep variant sites where at least one alternate allele is an indel (AC->GT is considered as an SNV not an INDEL).

Syntax :

--keep-indels

remove-indels

Remove variant sites where at least one alternate allele is an indel (AC->GT is considered as an SNV not an INDEL).

Syntax :

--remove-indels

keep-snvs

Keep variant sites where at least one alternate allele is an SNV (AC->GT is considered as an SNV not an INDEL).

Syntax :

--keep-snvs

remove-snvs

Remove variant sites where at least one alternate allele is an SNV (AC->GT is considered as an SNV not an INDEL).

Syntax :

--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

Variant with any of the listed Info Fields are kept

Syntax :

--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

Variant with all the listed Info Fields are kept

Syntax :

--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

Variant with any of the listed Info Fields are removed

Syntax :

--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

Variant with all the listed Info Fields are removed

Syntax :

--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

Keep variants with at least the number of specified alleles (reference plus alternates

Syntax :

--min-alleles number of alleles

Example

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

max-alleles

Keep variants with at most the number of specified alleles (reference plus alternates

Syntax :

--max-alleles number of alleles

Example

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

min-meanDP

Keep variants with a mean Depth of coverage across samples at least equal to the given value

Syntax :

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

Example

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

min-medianDP

Keep variants with a median Depth of coverage across samples at least equal to the given value

Syntax :

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

Example

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

max-meanDP

Keep variants with a mean Depth of coverage across samples at most equal to the given value

Syntax :

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

Example

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

max-medianDP

Keep variants with a median Depth of coverage across samples at most equal to the given value

Syntax :

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

Example

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

min-meanGQ

Keep variants with a mean Genotype Quality across samples at least equal to the given value

Syntax :

--min-meanGQ genotype-quality (integer)

Example

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

min-medianGQ

Keep variants with a median Genotype Quality across samples at least equal to the given value

Syntax :

--min-medianGQ genotype-quality (integer)

Example

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

max-meanGQ

Keep variants with a mean Genotype Quality across samples at most equal to the given value

Syntax :

--max-meanGQ genotype-quality (integer)

Example

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

max-medianGQ

Keep variants with a median Genotype Quality across samples at most equal to the given value

Syntax :

--max-medianGQ genotype-quality (integer)

Example

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

hwe

Keep variants with Hardy-Weinberg Equilibrium p-value above the given threshold

Syntax :

--hwe p-value (double)

Example

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

remove-hwe

Remove variants with Hardy-Weinberg Equilibrium p-value above the given threshold

Syntax :

--remove-hwe p-value (double)

Example

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

max-missing

Keep variant with at most the given ratio of missing genotypes

Syntax :

--max-missing ratio (double)

Example

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

min-missing

Keep variant with at least the given ratio of missing genotypes

Syntax :

--min-missing ratio (double)

Example

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

max-missing-count

Keep variant with at most the given number of missing genotypes

Syntax :

--max-missing-count integer

Example

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

min-missing-count

Keep variant with at least the given number of missing genotypes

Syntax :

--min-missing-count integer

Example

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

phased

Keep variant without unphased genotypes

Syntax :

--phased

remove-phased

Remove variant without unphased genotypes

Syntax :

--remove-phased

minQ

Keep variants with a quality (VCF column QUALITY) at least equal to the given value

Syntax :

--minQ quality (double)

Example

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

maxQ

Keep variants with a quality (VCF column QUALITY) at most equal to the given value

Syntax :

--maxQ quality (double)

Example

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

keep-info-value

Keep variants for which the expression if true. Syntax : type:KEY[OPERATOR]value Key is the name in the INFO field value is the string/int/decimal value Allowed types are

  • s for String

  • i for integer

  • f for decimal (float)

Allowed operators are

  • ‘=’ (for types s, i and f)

  • ‘!=’ (for types s, i and f)

  • ‘>’ (for types i and f)

  • ‘>=’ (for types i and f)

  • ‘<’ (for types i and f)

  • ‘<=’ (for types i and f)

Note

Special value “missing_field” allows to define rules when the INFO field is not available for this variant

Note

This filter is not well suited for annotation where multiple values are present (one per allele, for example).

Syntax :

--keep-info-value logical expression

Examples

--keep-info-value (i:DP>10&&f:FREQ<=0.1)||s:VARIANTTYPE!=SNP : Keep variants where (DP>10 AND FREQ<=0.1) OR VARIANTTYPE == “SNP”
--keep-info-value f:FREQ<=0.1||f:FREQ=missing_field : Keep variants where FREQ<=0.1 or FREQ is missing

remove-info-value

Remove variants for which the expression if true. Syntax : type:KEY[OPERATOR]value Key is the name in the INFO field value is the string/int/decimal value Allowed types are

  • s for String

  • i for integer

  • f for decimal (float)

Allowed operators are

  • ‘=’ (for types s, i and f)

  • ‘!=’ (for types s, i and f)

  • ‘>’ (for types i and f)

  • ‘>=’ (for types i and f)

  • ‘<’ (for types i and f)

  • ‘<=’ (for types i and f)

Note

Special value “missing_field” allows to define rules when the INFO field is not available for this variant

Note

This filter is not well suited for annotation where multiple values are present (one per allele, for example).

Syntax :

--remove-info-value logical expression

Examples

--remove-info-value (i:DP>10&&f:FREQ<=0.1)||s:VARIANTTYPE!=SNP : Remove variants where (DP>10 AND FREQ<=0.1) OR VARIANTTYPE == “SNP”
--remove-info-value f:FREQ<=0.1||f:FREQ=missing_field : Remove variants where FREQ<=0.1 or FREQ is missing