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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:
- Map reads of tumor and normal separately to get two sams
- Sort sams separately to get two bams
- MarkDuplicates separately to get two bams.
- Run IndelTargetCreator with the two bams together to get one intervals file
- Run IndelRealigner with the two bams together and use -nWayOut to get two bams
- Run BQSR on two bams separately
- 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!