.. _filters: 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 :** .. code-block:: bash --keep-pos chr[:start[-end]],... | **Examples** | :code:`--keep-pos 14` : *All variants from chromosome 14* | :code:`--keep-pos chr12` : *All variants from chromosome 12* | :code:`--keep-pos 10:145678` : *All variants at position 10:145678* | :code:`--keep-pos chr3:10000-20000` : *All variants in region 10000-20000 on chromosome 3* | :code:`--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 :** .. code-block:: bash --keep-positions filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --keep-bed filename.bed | **Example** | :code:`--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 :** .. code-block:: bash --keep-pos-overlap chr[:start[-end]],... | **Examples** | :code:`--keep-pos-overlap 14` : *All variants from chromosome 14* | :code:`--keep-pos-overlap chr12` : *All variants from chromosome 12* | :code:`--keep-pos-overlap 10:145678` : *All variants at position 10:145678* | :code:`--keep-pos-overlap chr3:10000-20000` : *All variants in region 10000-20000 on chromosome 3* | :code:`--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 :** .. code-block:: bash --keep-positions-overlap filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --remove-pos chr[:start[-end]],... | **Examples** | :code:`--remove-pos 14` : *All variants from chromosome 14* | :code:`--remove-pos chr12` : *All variants from chromosome 12* | :code:`--remove-pos 10:145678` : *All variants at position 10:145678* | :code:`--remove-pos chr3:10000-20000` : *All variants in region 10000-20000 on chromosome 3* | :code:`--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 :** .. code-block:: bash --remove-positions filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --remove-bed filename.bed | **Example** | :code:`--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 :** .. code-block:: bash --remove-pos-overlap chr[:start[-end]],... | **Examples** | :code:`--remove-pos-overlap 14` : *All variants from chromosome 14* | :code:`--remove-pos-overlap chr12` : *All variants from chromosome 12* | :code:`--remove-pos-overlap 10:145678` : *All variants at position 10:145678* | :code:`--remove-pos-overlap chr3:10000-20000` : *All variants in region 10000-20000 on chromosome 3* | :code:`--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 :** .. code-block:: bash --remove-positions-overlap filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --thin distance (integer no_units, kb or mb) | **Examples** | :code:`--thin 1000` : *avoids having sites closer than 1kb from each other* | :code:`--thin 1kb` : *avoids having sites closer than 1kb from each other* | :code:`--thin 5000000` : *avoids having sites closer than 5mb from each other* | :code:`--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 :** .. code-block:: bash --keep-sample Sample1,Sample2,... | **Example** | :code:`--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 :** .. code-block:: bash --remove-sample Sample1,Sample2,... | **Example** | :code:`--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 :** .. code-block:: bash --keep-samples filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --remove-samples filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --max-sample number-of-samples (integer) | **Example** | :code:`--max-sample 5` : *Keep only 5 samples at random* ---------- ped --- | Keep only the samples described in the given PED file (see file formats) | | **Syntax :** .. code-block:: bash --ped filename.ped | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --keep-family Fam1,Fam2,... | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --remove-family Fam1,Fam2,... | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --keep-sex sex (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --remove-sex sex (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --keep-phenotype phenotype (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --remove-phenotype phenotype (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --keep-group Group1,Group2,... | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --remove-group Group1,Group2,... | **Example** | :code:`--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 :** .. code-block:: bash --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 :** .. code-block:: bash --keep-filtered-geno Tag1,Tag2,... | **Example** | :code:`--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 :** .. code-block:: bash --remove-filtered-geno Tag1,Tag2,... | **Example** | :code:`--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 :** .. code-block:: bash --minDP depth-of-coverage (integer) | **Example** | :code:`--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 :** .. code-block:: bash --maxDP depth-of-coverage (integer) | **Example** | :code:`--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 :** .. code-block:: bash --minGQ Genotype Quality (integer) | **Example** | :code:`--minGQ 30` : *Sets genotypes to missing if GQ <30* ---------- maxGQ ----- | Sets genotypes to missing if GQ is above the given value | | **Syntax :** .. code-block:: bash --maxGQ Genotype Quality (integer) | **Example** | :code:`--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 :** .. code-block:: bash --min-maf frequency (double) | **Example** | :code:`--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 :** .. code-block:: bash --max-maf frequency (double) | **Example** | :code:`--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 :code:`--ped` .. warning:: Diploid variants expected | | **Syntax :** .. code-block:: bash --min-group-maf frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :code:`--ped` .. warning:: Diploid variants expected | | **Syntax :** .. code-block:: bash --max-group-maf frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :** .. code-block:: bash --min-ref-af frequency (double) | **Example** | :code:`--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 :** .. code-block:: bash --max-ref-af frequency (double) | **Example** | :code:`--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 :code:`--ped` .. warning:: Diploid variants expected | | **Syntax :** .. code-block:: bash --min-group-ref-af frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :code:`--ped` .. warning:: Diploid variants expected | | **Syntax :** .. code-block:: bash --max-group-ref-af frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :** .. code-block:: bash --min-all-non-ref-af frequency (double) | **Example** | :code:`--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 :** .. code-block:: bash --max-all-non-ref-af frequency (double) | **Example** | :code:`--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 :code:`--ped` .. warning:: Diploid variants expected | | **Syntax :** .. code-block:: bash --min-group-all-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :code:`--ped` .. warning:: Diploid variants expected | | **Syntax :** .. code-block:: bash --max-group-all-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :** .. code-block:: bash --min-any-non-ref-af frequency (double) | **Example** | :code:`--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 :** .. code-block:: bash --max-any-non-ref-af frequency (double) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --min-group-any-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --max-group-any-non-ref-af frequency (group1:af1,group2:af2,...,groupN:afN) | **Example** | :code:`--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 :** .. code-block:: bash --min-ref-ac allele-count (integer) | **Example** | :code:`--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 :** .. code-block:: bash --max-ref-ac allele-count (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --min-group-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --max-group-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :** .. code-block:: bash --min-all-non-ref-ac allele-count (integer) | **Example** | :code:`--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 :** .. code-block:: bash --max-all-non-ref-ac allele-count (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --min-group-all-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --max-group-all-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :** .. code-block:: bash --min-mac allele-count (integer) | **Example** | :code:`--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 :** .. code-block:: bash --max-mac allele-count (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --min-group-mac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --max-group-mac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :** .. code-block:: bash --min-any-non-ref-ac allele-count (integer) | **Example** | :code:`--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 :** .. code-block:: bash --max-any-non-ref-ac allele-count (integer) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --min-group-any-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :code:`--ped` | | **Syntax :** .. code-block:: bash --max-group-any-non-ref-ac allele-count (group1:ac1,group2:ac2,...,groupN:acN) | **Example** | :code:`--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 :** .. code-block:: bash --keep-id id1,id2,.... | **Examples** | :code:`--keep-id rs123456` : *variants with ID matching rs123456* | :code:`--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 :** .. code-block:: bash --remove-id id1,id2,.... | **Examples** | :code:`--remove-id rs123456` : *variants with ID matching rs123456* | :code:`--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 :** .. code-block:: bash --keep-ids filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --remove-ids filename.txt | **Example** | :code:`--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 :** .. code-block:: bash --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 :** .. code-block:: bash --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 :** .. code-block:: bash --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 :** .. code-block:: bash --remove-snvs keep-filtered-all ----------------- | to pass, all variant's Tags must be listed | sites removed by :code:`--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 :** .. code-block:: bash --keep-filtered-all Tag1,Tag2,... | **Example** | :code:`--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 :code:`--remove-filtered-any` are kept | | **Syntax :** .. code-block:: bash --keep-filtered-any Tag1,Tag2,... | **Example** | :code:`--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 :code:`--keep-filtered-all` are removed | | **Syntax :** .. code-block:: bash --remove-filtered-all Tag1,Tag2,... | **Example** | :code:`--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 :code:`--keep-filtered-any` are removed | | **Syntax :** .. code-block:: bash --remove-filtered-any Tag1,Tag2,... | **Example** | :code:`--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 :code:`--strict-remove-filtered-all` are kept | | **Syntax :** .. code-block:: bash --strict-keep-filtered-all Tag1,Tag2,... | **Example** | :code:`--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 :code:`--strict-remove-filtered-any` are kept | | **Syntax :** .. code-block:: bash --strict-keep-filtered-any Tag1,Tag2,... | **Example** | :code:`--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 :code:`--strict-keep-filtered-all` are removed | | **Syntax :** .. code-block:: bash --strict-remove-filtered-all Tag1,Tag2,... | **Example** | :code:`--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 :code:`--strict-keep-filtered-all` are removed | | **Syntax :** .. code-block:: bash --strict-remove-filtered-any Tag1,Tag2,... | **Example** | :code:`--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 :** .. code-block:: bash --keep-any-info Info1,Info2,... | **Example** | :code:`--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 :** .. code-block:: bash --keep-all-info Info1,Info2,... | **Example** | :code:`--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 :** .. code-block:: bash --remove-any-info Info1,Info2,... | **Example** | :code:`--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 :** .. code-block:: bash --remove-all-info Info1,Info2,... | **Example** | :code:`--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 :** .. code-block:: bash --min-alleles number of alleles | **Example** | :code:`--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 :** .. code-block:: bash --max-alleles number of alleles | **Example** | :code:`--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 accross samples at least equal to the given value | | **Syntax :** .. code-block:: bash --min-meanDP depth-of-coverage (integer) | **Example** | :code:`--min-meanDP 10` : *Keep variants with a mean DP accross samples at least equal to 10* min-medianDP ------------ | Keep variants with a median Depth of coverage accross samples at least equal to the given value | | **Syntax :** .. code-block:: bash --min-medianDP depth-of-coverage (integer) | **Example** | :code:`--min-medianDP 10` : *Keep variants with a median DP accross samples at least equal to 10* max-meanDP ---------- | Keep variants with a mean Depth of coverage accross samples at most equal to the given value | | **Syntax :** .. code-block:: bash --max-meanDP depth-of-coverage (integer) | **Example** | :code:`--max-meanDP 10` : *Keep variants with a mean DP accross samples at most equal to 10* max-medianDP ------------ | Keep variants with a median Depth of coverage accross samples at most equal to the given value | | **Syntax :** .. code-block:: bash --max-medianDP depth-of-coverage (integer) | **Example** | :code:`--max-medianDP 10` : *Keep variants with a median DP accross samples at most equal to 10* min-meanGQ ---------- | Keep variants with a mean Genotype Quality accross samples at least equal to the given value | | **Syntax :** .. code-block:: bash --min-meanGQ genotype-quality (integer) | **Example** | :code:`--min-meanGQ 10` : *Keep variants with a mean GQ accross samples at least equal to 10* min-medianGQ ------------ | Keep variants with a median Genotype Quality accross samples at least equal to the given value | | **Syntax :** .. code-block:: bash --min-medianGQ genotype-quality (integer) | **Example** | :code:`--min-medianGQ 10` : *Keep variants with a median GQ accross samples at least equal to 10* max-meanGQ ---------- | Keep variants with a mean Genotype Quality accross samples at most equal to the given value | | **Syntax :** .. code-block:: bash --max-meanGQ genotype-quality (integer) | **Example** | :code:`--max-meanGQ 10` : *Keep variants with a mean GQ accross samples at most equal to 10* max-medianGQ ------------ | Keep variants with a median Genotype Quality accross samples at most equal to the given value | | **Syntax :** .. code-block:: bash --max-medianGQ genotype-quality (integer) | **Example** | :code:`--max-medianGQ 10` : *Keep variants with a median GQ accross samples at most equal to 10* hwe --- | Keep variants with Hardy-Weinberg Equilibrium p-value above the given threshold | | **Syntax :** .. code-block:: bash --hwe p-value (double) | **Example** | :code:`--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 :** .. code-block:: bash --remove-hwe p-value (double) | **Example** | :code:`--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 :** .. code-block:: bash --max-missing ratio (double) | **Example** | :code:`--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 :** .. code-block:: bash --min-missing ratio (double) | **Example** | :code:`--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 :** .. code-block:: bash --max-missing-count integer | **Example** | :code:`--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 :** .. code-block:: bash --min-missing-count integer | **Example** | :code:`--min-missing-count 17` : *Keep variant with more than 17 missing genotypes* phased ------ | Keep variant without unphased genotypes | | **Syntax :** .. code-block:: bash --phased remove-phased ------------- | Remove variant without unphased genotypes | | **Syntax :** .. code-block:: bash --remove-phased minQ ---- | Keep variants with a quality (VCF column QUALITY) at least equal to the given value | | **Syntax :** .. code-block:: bash --minQ quality (double) | **Example** | :code:`--minQ 500` : *Keep variants with QUALITY >= 500* maxQ ---- | Keep variants with a quality (VCF column QUALITY) at most equal to the given value | | **Syntax :** .. code-block:: bash --maxQ quality (double) | **Example** | :code:`--maxQ 500` : *Keep variants with QUALITY <= 500*