I have HLA typed whole genome sequencing data using HLA-VBSeq. Reads were first aligned to hg19 with BWA-MEM, then reads aligning to all HLA loci and unmapped reads were extracted from the bam file using samtools. The extracted reads were then combined and re-aligned to the collection of all the genomic HLA allele sequences in the IMGT/HLA database using BWA-MEM, allowing for multiple alignments to the reference sequences.
Now, I would like to subset the reads of a specific HLA-E gene allele, however, using
samtools view input.bam HLA:HLA00936, I see that all of the sequences have a MAPQ score of 0. I know that this is specific to BWA and indicates that the reads are mapping to multiple locations. Does this mean that the alignment results for this allele are insignificant and should be disregarded? The researcher interested in this allele would like to know the HLA-E sequences for gene editing purposes, but I feel as though the coverage is far too low. Any input or advice is much appreciated.