Whole genome Pooled sequnce data analysis

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Tania Zahid

• May 17, 2020 09:04
• Edited

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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  Bhanu Gandham

  • May 18, 2020 01:17

  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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