Hi,
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!
I have changed your title to make it more specific.
If you want to know if the low coverage is related to the inversion, then compare the coverage to other (control) genomes from males?
I'm not sure if I follow here...
I didn't do WGS on any controls. This sample is a horse and we don't very much horse related project so I didn't want to spend the money to sequence a control. I figured if I could something I could do sanger sequence to confirm.
This was my thought process, and this could be incorrect since it is male sample there is obviously just one X all the reads in this region would be inverted. I am wondering if since these reads are inverted, they wouldn't map very well to the genome? I feel like that doesn't make sense though.
Why would that be the case?
Yeah... the more I think about it makes me think there is just poor coverage here :(