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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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SV calling on sex chromosomes #325

Open prasundutta87 opened 2 years ago

prasundutta87 commented 2 years ago

Hi,

I was just wondering if there is any specific methodology that needs to be followed before calling SVs on sex chromosomes using sniffles2? I am using a reference genome for SV calling in humans that has both X and Y chromosomes (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna). I know SNP calling on sex chromosomes is a different ball game than SNP calling in autosomes (due to PAR), but just wondering if anything specific needs to be taken into account while SV calling on the sex chromosomes. I am working with trios in my case.

Regards, Prasun

fritzsedlazeck commented 2 years ago

Hi, no we haven't planned any extra steps nor experimented with this. Obviously, keep in mind that the genotypes will handle the sex chromosomes like it would be autosomes..

Please keep me posted. I would be interesting to see if you find any issues.

Thanks Fritz

prasundutta87 commented 2 years ago

Thanks for this @fritzsedlazeck ..will keep you posted!

Regards Prasun