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tumor/normal best practice?

After reading the GATK forum and site extensively, I came up with a workflow that I think that might work:

  1. Map reads of tumor and normal separately to get two sams
  2. Sort sams separately to get two bams
  3. MarkDuplicates separately to get two bams.
  4. Run IndelTargetCreator with the two bams together to get one intervals file
  5. Run IndelRealigner with the two bams together and use -nWayOut to get two bams
  6. Run BQSR on two bams separately
  7. Run the two bams together with mutect to get the somatic SNPs

Is that it??? Anything wrong??

Two more questions:
1) Is it possible to run VQSR here?
2) If I add a high confidence somatic SNP vcf (e.g. Cosmic) to BQSR, will I improve the result of tumor BQSR?

Thanks a lot in advance!

Best Answer


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