Whole genome/exome association analysis toolset for annotated variants in next-generation sequencing studies

--memory {50000}:assign 50000 MB (around 50 GB) memory to run ATAV. The necessary memory size is dependent on the your dataset. You need to assign more than 50 GB memory to run a whole genome dataset, and about 30 GB memory to run a whole exome dataset.

--project {$PROJECT.gsap}: specify an SVA project gasp file, with gsap.sva and gsap.sva.data files in the same folder; $PROJECT.gsap is the SVA filename.

--list-trio-denovo: list de novo mutations in trios.

--min-coverage-screen {10} [optional]: specify a minimum coverage (read depth) for generating variant type/flag (de novo, newly homozygous); the default value is 10.

--min-case-cov-screen {0} [optional]: specify a minimum coverage for collecting qualified variants to calculate variant frequency in cases; the default value is 0.

--min-ctrl-cov-screen {10} [optional]: specify a minimum coverage for collecting qualified variants to calculate variant frequency in controls; the default value is 10.

--out {foldername & fileroot} [optional]: specify output foldername and output root filename; the default value is the project name.

--exclude-male-het [optional]: when "--exclude-male-het" is specified, variants on sex chromosomes that have one or more male(s) with heterozygous mutations will be excluded. By default, these variants are included but the questionable males are set to missing.

--exclude-tolerant [optional]: use a flag "--exclude-tolerant" to exclude NON_SYNONYMOUS_CODING variants that are predicted as "tolerant".

--ctrlMAF {0.05} [optional]: specify a maximum variant allele frequency in controls; the default value is 0.05. For example, if one user specifies "--ctrlMAF 0.05", ATAV will load variants that their frequencies are either <= 0.05 or >= 0.95. This is for loading rare variants and calculation of significance threshold for rare variants.

--snvFunctionList { STOP_GAINED, STOP_LOST,ESSENTIAL_SPLICE_SITE, NON_SYNONYMOUS_CODING} [optional]: specify snv functional list, using comma (,) to separate them (NOTE: don't add blank after comma); the default value is STOP_GAINED, STOP_LOST, ESSENTIAL_SPLICE_SITE, NON_SYNONYMOUS_CODING. The available snv functional list are in the following: STOP_GAINED, STOP_LOST, FRAMESHIFT_CODING, NON_SYNONYMOUS_CODING, ESSENTIAL_SPLICE_SITE, SPLICE_SITE, REGULATION_REGION, INTRONIC_EXON_BOUNDARY, 5PRIME_UTR, 3PRIME_UTR, EXONIC_NON_CODING_RNA, UPSTREAM, DOWNSTREAM, INTRONIC, SYNONYMOUS_CODING, INTERGENIC, REFERENCE, CANNOT_ANNOTATE. If you want to include all of the functional categories, you can use "--snvFunctionList full-list".

--indelFunctionList {CODING_DISRUPTED_FRAMESHIFT,CODING_DISRUPTED_OTHER} [optional]: specify indel functional list, using comma (,) to separate them (NOTE: don't add blank after comma); the default value is CODING_DISRUPTED_FRAMESHIFT, CODING_DISRUPTED_OTHER. The available indel functional list are in the following: CODING_DISRUPTED_FRAMESHIFT, CODING_DISRUPTED_OTHER, TRANSCRIPT_INCLUDED, 5PRIME_UTR, 3PRIME_UTR, INTRONIC_EXON_BOUNDARY, UPSTREAM, DOWNSTREAM, INTRONIC, INTERGENIC, CANNOT_ANNOTATE, SPLICE_SITE. If you want to include all of the functional categories, you can use "--indelFunctionList full-list".