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konradjk / exac_browser

Browser for ExAC consortium data
http://exac.broadinstitute.org
MIT License
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VCF format issue #269

Closed ghost closed 7 years ago

ghost commented 8 years ago

Hi - this is in reference to an issue in r0.3 that was said to be fixed in r.0.3.1. See https://github.com/konradjk/exac_browser/issues/164 https://github.com/konradjk/exac_browser/issues/230

Am using the r0.3.1 sites file ftp://ftp.broadinstitute.org/pub/ExAC_release/current/ExAC.r0.3.1.sites.vep.vcf.gz

and getting errors in AC_Het for sites with more than one allele in the ALT field.

INFO= ID=AC_Het,Number=A,Type=Integer,Description="Adjusted Heterozygous Counts"

Examples of errors from vcf-validator and the vcf rows INFO field at 1:13528 .. INFO tag [AC_Het=13,9,0] expected different number of values (expected 2, found 3) INFO field at 1:17478 .. INFO tag [AC_Het=24,1,0] expected different number of values (expected 2, found 3) 1 13528 . C G,T 1771.54 VQSRTrancheSNP99.60to99.80 ... AC_Het=13,9,0; 1 17478 . C T,G 4659.13 PASS ... AC_Het=24,1,0;

Should the tag be AC_Het,Number=R?

thx, pfs

ghost commented 8 years ago

Oops. just saw https://github.com/konradjk/exac_browser/issues/256, same issue

konradjk commented 7 years ago

This is now fixed with release 1.0 - sorry for the delay!