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how to solve a problem with the depthofcoverage input format?

Hello, I´m trying to use deptofcoverage to check the coverage of my reads. I already have the indexed bam files (created with sam to bam) and also reordered (reorder SAM/BAM) but they are still not recognized by depthofcoverage and I got this error message:

"Sequences are not currently available for the specified build"

I used "human (homo sapiens) hg19 full" for mapping but I can´t select it, it only allows b37 version.

Any suggestions?

Thank you very much in advance

Gema

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Gema,

    Are you using GATK via Galaxy? If so we can't help you, you'll need to ask the Galaxy support staff for help.

    If it turns out that you can't use hg19 via Galaxy, you should consider using command-line GATK instead. You will be able to use hg19, as well as a much more recent and improved version of the GATK tools.

  • ge2sasagge2sasag Member

    Hi! yes I´m using GATK through Galaxy, so I will ask them, thank you very much for your answer

    Best,
    Gema

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