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Set up pipeline for WES and WGS

manolismanolis Member ✭✭
edited October 2018 in Ask the GATK team


working with WES and WGS data (GATK I would like to know the set up differents between their pipelines for germline and somatic variant discovery.

I saw that I have to use two different interval lists (-L, BQSR & HC), as also in the VQSR step I have to exclude the -an DP option in the WES pipeline .

Moreover, in the site it is reported that there is a WES pipeline with hg19 and a WGS pipeline with hg38, in which the last one is in the Best Practices pages.

Could you provide me any link about the WES set up.

Many thanks

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