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Pipeline for familial sequencing

We had several samples sequenced and aligned separately and I would like to resequence the data together now that we have data from all family members -- looking for advice on what pipeline to use as a best practice. The sequencing was done as follows:

  • Mom + Son sequenced / analyzed together (2 BAMs, 2 VCFs)
  • Dad + Sister 1 + Sister 2 sequenced / analyzed together (3 BAMS, 3VCFs)
  • Sister 1 + Brother 1 sequenced / analyzed together (2 BAMS, 2VCFs)

The goal here is to detect denovo variants. My understanding is that the best practice would be to analyze all 7 samples together (alignment + variant calling). I am not sure how to best do the alignment and variant calling myself on a familial sample taking into account pedigree.

ngs
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updated by Brice Sarver Brice Sarver • written by saliksyed88 • saliksyed88

1 answer

You can start by doing joint variant calling among the family members. This will give you increased confidence that a variant is truly de novo in a proband or relative. The GATK has workflows for this, and you may also want to check out this publication for some background (though it's focusing on complex variation).

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written by Brice Sarver Brice Sarver

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