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Trio Report ATAV Command

The trio report incorporates information the ATAV trio screen, non-Trio data identifying pathogenic variants ignoring inheritance, a parental mosaic screen, and parent variant information to check for inheritance. These different data sources need to be run as separate ATAV commands

Trios

As of ATAV version 6.5 there is a single command to execute trio de novo, hemizygous, homozygous and compound heterozygous screens.

 atav.sh --list-trio --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-coverage 10 --qual 30 --qd 1 --gq 20 \
--exclude-evs-qc-failed --exclude-artifacts --include-qc-missing --include-known-var --include-rvis --include-sub-rvis --include-gerp --include-mgi --include-trap \
--include-denovo-db --disable-check-on-sex-chr --include-gnomad-genome --include-gnomad-exome --include-discovehr --include-mtr --sample <sample file> --out <desired output file location>

trio-Non-Trio

trio-Non-Trio input file should only include probands

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-coverage 10 --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 --disable-check-on-sex-chr --case-only --include-discovehr --include-mtr --sample <nonTrio sample file> --out <desired output file location>

Parental Mosaic

atav.sh --effect /nfs/goldstein/software/atav_home/data/effect/codingandsplice.txt --ctrl-af 0.0005 --evs-maf 0.0005 --exac-af 0.0005 --exac-pop global,afr,amr,eas,sas,fin,nfe \
--filter pass,likely,intermediate --exclude-evs-qc-failed --exclude-artifacts --qual 30 --mq 40 --rprs -4 --mqrs -8 --child-qd 2 --child-het-percent-alt-read 0.30-0.80 --min-child-binomial 0.1 \
--max-parent-binomial 0.00001 --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 --disable-check-on-sex-chr --list-parental-mosaic --sample <sample file> --out <desired output file location>

Parent

Parent input file should only include parents set as cases

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-coverage 10 --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 --disable-check-on-sex-chr --case-only --include-discovehr --include-mtr--sample <parent sample file> --out <desired output file location>