Closed a113n closed 10 years ago
Allen;
Thanks much for the report and apologies about the issue. I pushed a fix that will avoid the subset when more than one sample is present. This allows multi-sample inputs into variant-prep
and will hopefully do what you need. I created a new snapshot if you have time to test and we'll roll this into the next release:
Thanks again.
Hi Brad,
I am not sure if "variant-prep" supports the normalization of multi-sample VCF. I tried to run "variant-prep" on a multi-sample VCF generated by GATK 3.0, however only the genotype calls of the first sample exist in the output.
It looks like the culprit lies in the SelectVariants step, where only the first sample is specified in the parameter "--sample_name". Here attached the output excerpt:
FYI, I am using bcbio.variation v0.1.7-SNAPSHOT-20140518. I hope you can give me some hints on this issue, thank you very much!
Best regards, Allen