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Convert Mutect1 output to VCF

eeuzceeuzc SwitzerlandMember

Hi Geraldine & Sheila,

I have run Mutect1 (1.1.7) on whole genome sequences and got the output as a text file. Is there a way to convert this to VCF?
I found out now that one can specify --vcf argument while running Mutect. But is there a way to convert after the run. I don;t want to repeat the analysis.



  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi!! :smile:

    It depends. Did you simply output the MuTect1 output to a .txt file? In that case, it is a proper VCF with the incorrect extension, so you can simply change the .txt to a .vcf.

    Can you post a few lines from your .txt file?


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