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SNP Calling in pooled samble
HI every body!
I have perform a target DNAseq panel (aligment with BWA) and I have sampled pooled without index. I'm analysing my positive control (It has variants that I know that are real). I detect all in IGV. But I only detect 50% using HaplotypeCaller I have change several parameter as --minDanglingBranchLength =1.
One of the variant that I need detect have 50 read for mutated allele and 975 for the reference allele. So my variant is in the 5% of my read.
Any idea to detect this king of variants?
Thank you so much in advance!!!!!