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samtools / bcftools

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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[W::bcf_calc_ac] Incorrect number of AC fields at Chrxx:xxxxx. (This message is printed only once.) #2159

Closed leeleeleeaaaaaaaaaalee closed 2 months ago

leeleeleeaaaaaaaaaalee commented 2 months ago

Hi,

Thank you for inventing this tool for effective genomic analysis. However, I have encountered some issues on it. I attempted to use bcftools for subsetting 300 samples from my raw vcf, which carries 500 samples. Here is the code trying to reach that purpose: bcftools view -S "sample_list.txt" "vcf_passed.vcf.gz" | bgzip -c > "vcf_passed_subset.vcf.gz". I did receive the result and the subsetted vcf also looks fine, but followed by an error message:[W::bcf_calc_ac] Incorrect number of AC fields at Chrxx:xxxxx. (This message is printed only once.).

May I know if it is fine and how I can solve the problem. Thanks!!

pd3 commented 2 months ago

This is a common problem with VCFs broken in a very specific way, please check the description of this problem and how to fix in the FAQ here http://samtools.github.io/bcftools/howtos/FAQ.html#incorrect-nfields