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Can I force GATK UG to call SNP / Indel on a aligned bac contig (coverage of 1)?

WimSWimS Member ✭✭

Can I force GATK UG to call SNP / Indel on a aligned bac contig (coverage of 1)? I tried to put -stand_call_conf and -stand_emit_conf on zero but I stil got a vcf file with just a header and no calls.

I have aligned a BAC contig with BWA mem to a reference sequence and I want to extract the SNP's and Indels that the BAC contig supports.

When I have those SNPs and InDels in a vcf file I can use them together with my SNP and INdels from NGS data to get the genotype concordance (with the genotype concordance tool. )

And I can use them for VQSR.

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm, GATK isn't really designed with that in mind, but let's see... what does the bam file with your contig look like? Does it have a mapping quality, base quality scores etc? The UG needs those to be able to run its model.

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