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Genotype Level Filter Options

--min-coverage: specify a minimum coverage (read depth), applied to DP Bin. (Only accept value 10, 20, 30, 50, 200)

--filter: PASS, LIKELY, INTERMEDIATE, FAIL (using comma delimited)

--het-percent-alt-read: this filter will exclude the het variants by the alt read freq. (input Ex. 0.4-0.6 or 0.2-0.8)

--hom-percent-alt-read: this filter will exclude the hom variants by the alt read freq. (input Ex. 0.4-0.6 or 0.2-0.8)

--min-percent-alt-read-binomial-p: specify a minimum percent alt read binomial P value.

--max-percent-alt-read-binomial-p: specify a maximum percent alt read binomial P value.

--min-gq: specify a minimum genotype_qual_GQ.

--max-sor: specify a maximum strand Odds ratio.

--max-snv-sor: specify a minimum strand Odds ratio for SNVs.
--max-indel-sor: specify a minimum strand Odds ratio for indels.

--max-fs: specify a maximum strand_bias_FS.

--max-snv-fs: specify a maximum strand_bias_FS for SNVs.
--max-indel-fs: specify a maximum strand_bias_FS for indels.

--min-mq: specify a minimum rms_map_qual_MQ.

--min-qd: specify a minimum qual_by_depth_QD.

--min-qual: specify a minimum qual.

--min-rprs: specify a minimum read_pos_rank_sum.

--min-mqrs: specify a minimum map_qual_rank_sum.

-–include-qc-missing: this option will make the qc filter only apply to existing qc value samples and treat those missing qc value samples as 'PASS'.

If you use any quality filters in ATAV, then samples with variants that are missing scores for those fields will have their genotypes for those variants set to missing. if you want to include them, use the --include-qc-missing option.

--include-hom-ref: use this option to have ATAV included Hom Ref genotype, default only included Hom or Het.