Open jodyphelan opened 2 years ago
I have found an issue with the vcf format output by pilon. Using bcftools view -c 1 pilon.vcf it complains with the error:
bcftools view -c 1 pilon.vcf
[E::bcf_calc_ac] Incorrect allele ("1") in SAMPLE at Chromosome:767398
This seems to be related to this line in the vcf:
Chromosome 767398 . C . . Del DP=0;TD=44;BQ=0;MQ=60;QD=0;BC=0,0,0,0;QP=0,0,0,0;PC=114;IC=0;DC=44;XC=0;AC=2;AF=0.00 GT 1/1
The GT field indicates the alternate is present, but the alternate is set to '.'
Is this valid VCF format?
I have found an issue with the vcf format output by pilon. Using
bcftools view -c 1 pilon.vcfit complains with the error:This seems to be related to this line in the vcf:
The GT field indicates the alternate is present, but the alternate is set to '.'
Is this valid VCF format?