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AC,AF, and AN INFO fields are not defined in output from HaplotypeCaller

davidwbdavidwb Park City, UTMember


I have a problem where the output vcf from the haplotypecaller doesn't include meta-information lines for the AC,AF, and AN info fields, yet one of the records in the vcf contains these info fields.

$ grep -e "##INFO=<ID=AC" NA12878-I9_16_chr6.variant.vcf
$ grep -e "AC=2;" NA12878-I9_16_chr6.variant.vcf
chr6    15613333    rs145086187    TGC    AGT    331.78    PASS    AC=2;AF=1.00;AN=2    GT:GQ    1/1:24

How can I get the haplotypecaller to add the meta-information lines for these info fields?




  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi David,

    Are you saying that with the latest version of HaplotypeCaller, the output VCF does not contain those annotation descriptions in the header? Can you please post the exact command you ran?


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