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

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

    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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