Question about idr_baf
mingoo426 opened this issue · comments
Hi there!
I'm a student who's new in bioinformatics/genetics/github and I apologize in advance if this is not the right place to ask questions.. (if there's a forum where I could ask about peddy, I'll relocate this to that forum)
But I wanted to ask about idr_baf.
Question 1. According to the documentation for the inter-decile range, it states: "Large values indicated likely sample contamination.". But isn't this already fulfilled from the het_call / median depth graph? What additional insight can we get from the idr_baf that we cannot get from the graph?
Question 2. About heterozygosity. "Large values indicated likely sample contamination.". When you say large value, is this relative to the other samples? Or is this relative to the heterozygosity of a typical genomic sample of humans?
Thank you so much!
Best,
Min Ku
Hi Min,
-
this is just another measure. the heterozygosity and the IDR_BAF should be correlated, but sometimes only one is high
-
yes, relative to other samples. so often you can see outliers in your cohort.
(also check out somalier which is the successor to peddy).
thank you so much! :)
Hi Brent, would it be ok to ask just one more question?
I noticed that on the 'het / homo for X chromosome graph', for most of my male samples, the ratios were not 0 (but close enough). I checked my vcf file and some of the male samples actually had het calls for some of the variants on the non-PAR regions of the X chr.
I thought why this is so (they are supposed to have 0 het calls theoretically, right?)
- for some reason, the reads that came from autosome somehow got aligned to X-chromosome?
- Sequencing error? (mutation was introduced in the read at the hard-to-read region? or homopolymeric region such as CCCCCC?)
These are some of the reasons I came up with... am I thinking in the right direction?
Hi, yes, the reasons for hets in males on X is most likely error in alignment and variant calling.
thank you! :)