Hi everyone,

I just want to confirm what I got back from HaplotypeCaller (GATK 3.7) is correct format, it is VCF4.2 format, however, after following the best practice, I have a vcf file with the GT field with "/" not "|", according to the VCF4.2 format, the "/" means unphased genotype, however, haplotypeCaller should provide haplotype calls instead of genotypes right? Should I use the results as unphased or phased?

Here are couple lines from the vcf file generated.

fileformat=VCFv4.2

...

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

1 10492 . C T 39.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.385;ClippingRankSum=0.000;DP=7;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.37;MQRankSum=-1.282;QD=6.63;ReadPosRankSum=0.000;SOR=0.693 GT:AD:DP:GQ:PL 0/1:3,3:6:66:68,0,66

Thanks a lot!