I am working with about 500 samples of human exome data. used hg19 to align my reads and ran a standard best-practices GATK workflow. Later only to realise that a small 1Mb loci has not mapped properly due to the presence of a haplotype specific contig in the hg19 FASTA.
How do I force HaplotypeCaller or BCFTools to call a variant with mapping quality 0? I have disabled the read filters but that does not work. I just want the variants from one particular gene and since I have 500 samples, re-aligning them to a modified reference is not an option at the moment due to time constraints. I am aware of false positives occurring but we will validate any variants seen.
This is the command I've tried on BCFtools:
bcftools mpileup -q 0 -f ucsc.hg19.fasta file.bam -r chr17:43000000-45000000 | bcftools call -mv > file.vcf
this only outputs variants with MQ =/= 0