I would like to know regarding the effect of read group on Haplotype caller. Here, I have shown an example, I have more samples in the same scenario.
516_FCH7L2KCCX2_L7_BISvveXAAEBAAA-91 and 516_BISvveX_2nd are two different samples. ID, SM, and PL are the same for both samples, but LB and PU are different for both samples. Will they be considered the same sample during Haplotype caller? Will there be any effect on variant numbers using Haplotype caller? Kindly help me regarding this issue :)
First Sample name -> 516_BISvveX_2nd
@RG ID:E00591_309_H7L2KCCX2_7 SM:516 PL:ILLUMINA LB:516_BISvveX PU:E00591_309_H7L2KCCX2_7.516_BISvveX
Second sample name -> 516_FCH7L2KCCX2_L7_BISvveXAAEBAAA-91
@RG ID:E00591_309_H7L2KCCX2_7 SM:516 PL:ILLUMINA LB:516_FCH7L2KCCX2 PU:E00591_309_H7L2KCCX2_7.516_FCH7L2KCCX2
Thank you so much in advance
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