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GenotypeGVCF possible on just one chromosome?

medgenmedgen NorwayMember

I have a batch of g.vcf-files that I want to merge to one common vcf, but have a problem with error msg (one of these "please do NOT post-errors; "the provided VCF file is malformed at approximately line number..." ). I am not able to find the error. (standard "best practice"-GenotypeGVCF script that have worked a number of times in smaller groups of files). If problems-the program does not always tell me which file is the problem - but it indicate this time that the problem is on X - which is analyzed in the end of the run. This means that I have to wait ~week to get the error message. (I am using GATK 3.8, and Java/jdkl.8.0_112)

So I have been testing smaller groups of files to find the problem file - but It would be much faster to check the most likely chromosome only? Possible?
Would making a vcf from a single g.vcf detect the all same errors as genotyping groups of files?


  • medgenmedgen NorwayMember

    Sorry, I found and successfully used the "-L" argument , -it was not obvious from the documentation that this could be used also in GenotypeGVCFs. So that part is resolved.
    But I am still looking for the error. I get the "malformed"- error above when trying to generate the final combined vcf.file. However, each of those files have been successfully been included in smaller batches of files without error.

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