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Non-Trio Report ATAV Command

The non-Trio report will generate output for all affected cases. Parents will be run and added to a separate tab to check for inheritance.

Non-Trio

>atav.sh --list-var-geno --effect /nfs/goldstein/software/atav_home/data/effect/codingandsplice.txt --ctrl-af 0.01 --filter pass,likely,intermediate\
 --evs-maf 0.01 --exac-af 0.01 --exac-pop global,afr,amr,eas,sas,fin,nfe --min-ad-alt 3 --qual 30 --qd 2 --gq 20\
 --exclude-evs-qc-failed --exclude-artifacts --include-qc-missing --include-known-var --include-evs --include-exac --include-gnomad-genome\
 --include-gnomad-exome --include-gerp --include-rvis --include-sub-rvis --include-mgi --include-trap --include-denovo-db --include-discovehr\
 --include-mtr --include-revel --include-limbr --disable-check-on-sex-chr --case-only --sample <nonTrio sample file> --out <desired output file location>

Non-Trio Parents

>atav.sh --list-var-geno --effect /nfs/goldstein/software/atav_home/data/effect/codingandsplice.txt --ctrl-af 0.01 --filter pass,likely,intermediate\
 --evs-maf 0.01 --exac-af 0.01 --exac-pop global,afr,amr,eas,sas,fin,nfe --min-ad-alt 3 --qual 30 --qd 2 --gq 20\
 --exclude-evs-qc-failed --exclude-artifacts --include-qc-missing --include-known-var --include-evs --include-exac --include-gnomad-genome\
 --include-gnomad-exome --include-gerp --include-rvis --include-sub-rvis --include-mgi --include-trap --include-denovo-db --include-discovehr --include-mtr\
 --include-revel --include-limbr --disable-check-on-sex-chr --case-only --sample <nonTrio Parent sample file> --out <desired output file location>