Hi, would it be possible to force the output of sites that are 0/0 when given a vc

In "callVarBam.py", change <div class="snippet-clipboard-content notranslate posi

Output monomorphic sites when used with Known variant vcf about clair HOT 2 CLOSED

hku-bal commented on June 11, 2024

Output monomorphic sites when used with Known variant vcf

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Comments (2)

aquaskyline commented on June 11, 2024 1

In "callVarBam.py", change

    call_variant_command_options = [
        taskSet,
        ExecuteCommand('python', CVBin),
        CommandOption('chkpnt_fn', chkpnt_fn),
        CommandOption('call_fn', call_fn),
        CommandOption('bam_fn', bam_fn),
        CommandOption('sampleName', sampleName),
        CommandOption('threads', numCpus),
        CommandOption('ref_fn', ref_fn),
        pysam_for_all_indel_bases,
        haploid_mode,
        qual,
        debug
    ]

    call_variant_command_options = [
        taskSet,
        ExecuteCommand('python', CVBin),
        CommandOption('chkpnt_fn', chkpnt_fn),
        CommandOption('call_fn', call_fn),
        CommandOption('bam_fn', bam_fn),
        CommandOption('sampleName', sampleName),
        CommandOption('threads', numCpus),
        CommandOption('ref_fn', ref_fn),
        pysam_for_all_indel_bases,
        haploid_mode,
        qual,
        debug,
        "--showRef"
    ]

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jd3234 commented on June 11, 2024

Thanks for the quick reply!

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Output monomorphic sites when used with Known variant vcf about clair HOT 2 CLOSED

Comments (2)

Related Issues (20)

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