[E::vcf_parse_format] Invalid character 'N' in 'AC' FORMAT field

Question

[balathumma10]

The vcf file produced from SNVer has "NA"s in AC FORMAT field of some samples. Running bcftools with this vcf produces this error. Seems like bcftools is not expecting NA in AC field. Could someone please suggest a solution for this.

bcftools view test.vcf -i NP=8 -o test_NP8.vcf

[E::vcf_parse_format] Invalid character 'N' in 'AC' FORMAT field at scaffold_1:345947

Answer 1

[Pierre Lindenbaum]

look at the definition of AC in the header. it should be something like:

##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">

AC should be an Integer, not a string.

[balathumma10]

Here is the AC header

FORMAT=<id=ac,number=1,type=integer,description="alternative allele="" count"="">

[Pierre Lindenbaum]

yeah, so in your VCF you shouldn't find AC=N for scaffold_1:345947

[balathumma10]

when the DP is 0 the AC field has NA which could be 0. Not sure how to change NA to 0.

[Pierre Lindenbaum]

something like sed 's/AC=NA/AC=0/g'

[balathumma10]

Thank you very much. That solved the problem.

[Pierre Lindenbaum]

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