I apologize in advance for the vague titled. I did some WGS on a sample that had an interesting disease. The disease is X-linked and the sample was taken from a male. There have been a couple of papers published about this disease and they found a large inversion ~3kb in an intron. I was looking at the raw
.bam file and coverage gets pretty low, next to none, in the same region described in previous papers. So I am wondering if it is just a coincidence or maybe the software I used has trouble mapping that inversion since its a male and all the reads would be inverted due to hemizygosity.
I used bwa for aligning the reads, picard to sort/dedup, and samtools for variant calling.
I saw that pindel is a potential piece of software I could use but I saw that it uses bam files, which I can already tell has poor coverage in the area of interest. I think I have to use something other than bwa?
I could be completely wrong here, maybe bwa does a good job a mapping reads like this and there is just poor coverage in this region. I just think it is interesting there is poor coverage in this region. This region doesn't seem to have repeated sequences either so I doubt it is difficult to sequence.
Let me know what you think!