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Cohort Level Filter Options

--sample: specify a sample file to include all your interested samples and their case/ctrl and family status.

file format: Family ID, Individual ID, Paternal ID, Maternal ID, Sex, Phenotype, Sample Type, Capture Kit (tab delimited)

Family ID: specify a family id or use the same value as Individual ID to indicate this sample used as a non family control or case
Individual ID: sample name (child)
Paternal ID: sample name (father) or 0 (indicate not available)
Maternal ID: sample name (mother) or 0 (indicate not available)
Sex: 1=male,2=female
Phenotype: 1=control, 2=case
Sample Type & Capture Kit: please use the value form seqdb, including “N/A” for genome samples
Ex. /nfs/goldstein/software/atav_home/data/sample/ALS_1424_DukeGr_ctrl.txt

--include-default-control-sample: use this option to include 10908 control samples for the analysis.

--exclude-low-quality-sample: use this option to exclude samples meet below criteria.

(ContaminationPercentage > 8 & MeanCoverage < 200) or ContaminationPercentage > 15 or CCDSBasesCov10X < 50

--exclude-igm-gnomad-sample: use this option to exclude all IGM gnomAD samples from your sample file when using gnomAD filters.

Reference: /nfs/goldstein/software/atav_home/data/sample/igm_gnomad_sample_062620.txt (ATAV 7.1.4+)
Reference: /nfs/goldstein/software/atav_home/data/sample/igm_gnomad_sample.txt (ATAV 7.0.11 - 7.1.3)

--max-ctrl-af: specify a maximum variant allele frequency in controls. For example, if one specifies "--ctrl-af 0.05", ATAV will keep variants with frequencies that are <= 0.05.

--min-ctrl-af: specify a minimum variant allele frequency in controls. For example, if one specifies "--min-ctrl-af 0.05", ATAV will keep variants with frequencies that are >= 0.05.

--max-ctrl-maf: specify maximum minor allele frequency in controls. For example, if one specifies "--max-ctrl-maf 0.05", ATAV will keep variants with frequencies that are either <= 0.05 or >= 0.95.

--max-case-af: specify a maximum variant allele frequency in cases. For example, if one specifies "--case-af 0.05", ATAV will load variants with frequencies that are <= 0.05.

--max-af: specify a maximum variant allele frequency in samples (controls + cases). For example, if one specifies "--max-af 0.05", ATAV will keep variants with frequencies that are <= 0.05.

--min-af: specify a minimum variant allele frequency in samples (controls + cases). For example, if one specifies "--min-af 0.05", ATAV will keep variants with frequencies that are >= 0.05.

--max-maf: specify maximum minor allele frequency in samples (controls + cases). For example, if one specifies "--max-maf 0.05", ATAV will keep variants with frequencies that are either <= 0.05 or >= 0.95.

--min-maf: specify minimum minor allele frequency in samples (controls + cases). For example, if one specifies "--min-maf 0.05", ATAV will keep variants with frequencies that are > 0.05 and < 0.95.

--max-ac: specify maximum allele count per variant.

--min-ac: specify minimum allele count per variant.

--min-covered-case-percentage: specify a minimum covered case sample percentage [1, 100].

--min-covered-ctrl-percentage: specify a minimum covered control sample percentage [1, 100].

--min-variant-present: consider variants only if observed $N or more times in either het or hom when reference allele is major & het or ref when reference allele is minor. Default setting is 1.

--min-case-carrier: would require that the carriers of the variant be cases. if you set --min-case-carrier 2, the variant would need to be seen in at least 2 cases for it to be considered.

--max-qc-fail-sample: specify a maximum qc fail sample number.

QC Fail Case + QC Fail Ctrl <= above input value