Whole genome Pooled sequnce data analysis
Hii, Please tell me if GATK pipeline could be run on whole genome pooled sequence data? If yes, then kindly share the GATK pipeline for it.
Thanks
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Hi Tania Zahid
We do not have a pooled samples variant calling pipeline. We think Mutect2 should work since it takes into account probabilistic fluctuations in the proportional coverage, i.e. not assume that exactly X% of reads come from each of the 100/X samples. We have not tested this on our end so please use at your own discretion.
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