Open saphiecor opened 2 years ago
SnpEffVersion="5.0e (build 2021-03-09 06:01)"
ANN[].Allele does not match with GEN[].GT of sample.
on the vcf file (attached as txt file), it shows:
#CHROM POS ID REF ALT FORMAT S1 S2 S3 Chr6 1789051 . CTTTTT CTTTT,C GT:AD:DP:GQ:PL 1/1:1,8,0:9:7:153,7,0,156,24,173 2/2:0,0,17:17:51:715,715,715,51,51,0 2/2:0,0,20:20:60:901,901,901,60,60,0
but on the file output of extractFields command, the output looks like this:
CHROM POS REF ALT GEN[S1].GT GEN[S2].GT GEN[S3].GT ANN[S1].ALLELE ANN[S2].ALLELE ANN[S3].ALLELE ANN[S1].IMPACT ANN[S2].IMPACT ANN[S3].IMPACT Chr6 1789051 CTTTTT CTTTT,C 1/1 2/2 2/2 C C CTTTT MODIFIER MODIFIER MODIFIER
haplotypeCaller.txt
SnpEffVersion="5.0e (build 2021-03-09 06:01)"
ANN[].Allele does not match with GEN[].GT of sample.
on the vcf file (attached as txt file), it shows:
but on the file output of extractFields command, the output looks like this:
haplotypeCaller.txt