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.