We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

VCF FILE: Variant Called BUT none of the samples has it

MaguelonneMaguelonne ParisMember ✭✭


I've been running a calling on 200 samples following the recommended steps (https://software.broadinstitute.org/gatk/documentation/article.php?id=3893).

1) I've run the variant calling with HC on each sample's bam file with -mbq option set at 20;
2) I've run CombineGVCFs on the 200 .g.vcf files;
3) I've run GenotypeGVCFs on the combined .g.vcf with -stand-call-conf option set at 0.

I just had a look at the final VCF file and here's a line that I don't understand:
chr1 10297 . C T,* 29.53 . AC=2,0;AF=5.000e-03,0.00;AN=400;DP=23704;(...)

How could the variant **C>*** be called if none of the samples has it ?!

Thank you in advance for your help,




Sign In or Register to comment.