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verifyBamID can't handle missing trailing fields of sample #13
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Yes, you are right. But at the moment we have not enough hands to amend this feature. You are more than welcome to help to contribute to this package. Otherwise, you can try to use a script to fill in the field in your specific vcf file. We will try to fix this maybe later this semester. |
I see the point. I am also quite busy right now, but I can extend the error message and link a script which adds the missing fields. Just have to find/create. Or do you know a tool that does this? |
Unfortunately no, if you finished this script, you can try to create a pull request. Thanks! |
I just analyzed a VCF file created with GATK 3.8 pipeline and got the following error:
It turned out that this error occurs because GATK CombineGVCFs drops trailing fields per sample if they are empty. Apparently, this is allowed by the VCF format specification: https://gatkforums.broadinstitute.org/gatk/discussion/4149/format-fields-and-sample-entries-in-vcf-files#latest
Is there a parameter to ignore incomplete sample information?
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