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HaplotypeCaller bugs

E.ScienceE.Science London, UKMember


I have tried to solve several issues which came up while trying to run the HaplotypeCaller. For this one, I didn't find anything on google and to be honest when pasting the error, google doesn't even find something similar.

ERROR MESSAGE: Badly formed genome loc: Contig NC_007605 given as location, but this contig isn't present in the Fasta sequence dictionary

Can anyone please tell me what's the problem here? The fasta file I got was the one downloaded from the bundle: human_g1k_v37.fasta.gz

Any help would be really appreciated. Thank you!!

Best Answers


  • E.ScienceE.Science London, UKMember

    Thank you Geraldine. I tried using -XL NC_007605 as my option but I got the error:

    ERROR MESSAGE: Badly formed genome loc: Contig 'NC_007605' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?

    In which way can I exclude NC_007605 or just let the HC ignore it?

    Thank you.

  • E.ScienceE.Science London, UKMember

    Thank you very much! I actually did that and solved the problem!

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