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List ExAC

Command examples:

atav.sh --list-exac --variant PATH_TO_YOUR_VARIANT_FILE --out PATH_TO_OUTPUT_DIR

atav.sh --list-exac --region PATH_TO_YOUR_REGION_FILE --out PATH_TO_OUTPUT_DIR

Command options:

--list-exac: trigger list exac function.

--variant: use a variant id file (one id per line) or a variant id list (comma delimited)

id format: chr-pos-ref-alt

--region: use a region file or a region list (comma delimited)

region format: chr:start-end

--exac-pop is to specify which population (global, afr, amr, eas, sas, fin, nfe or oth) should be used for the exac maf cutoff. you can require the cutoff to be met in multiple populations by putting a comma between them, for example --exac-pop afr,amr,nfe.

--exac-maf is to specify a threshold and it will require variants to pass the threshold in all populations from --exac-pop

--min-exac-vqslod-snv is to specify a threshold and ATAV will only keep the SNVs if exac vqslod score is larger than the threshold.

Accordign to ExAC (ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.1/README.known_issues): The VQSR 99.6% SNP Sensitivity is too conservative and filters ~17% of singletons. Our analysis of singleton TiTv, Doubleton transmission in Trios, validated de-novo mutations and comparison against PCR-Free WGS has shown filtering ~10% of singletons is a better trade off. This corresponds to VQSLOD > -2.632: we recommend using --min-exac-vqslod-snv -2.632 for all analyses.

--min-exac-vqslod-indel is to specify a threshold and ATAV will only keep the indelif exac vqslod score is larger than the threshold.

SNV and indel VQSLODs are calculated separately, so separate cutoffs are required. We recommend using --min-exac-vqslod-indel 1.2168 to fit with the 95% tranche cutoff we use for our genome indels, which is what ExAC used for their data.

Output:

exac.csv

  • Variant ID
  • ExAC global maf
  • ExAC global gts
  • ExAC afr maf
  • ExAC afr gts
  • ExAC amr maf
  • ExAC amr gts
  • ExAC eas maf
  • ExAC eas gts
  • ExAC sas maf
  • ExAC sas gts
  • ExAC fin maf
  • ExAC fin gts
  • ExAC nfe maf
  • ExAC nfe gts
  • ExAC oth maf
  • ExAC oth gts
  • ExAC vqslod
  • ExAC Mean Coverage
  • ExAC Sample Covered 10x