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