I am currently working on a project where we have cancer and normal patient samples, in which we developed a pipeline for variant calls for SNPs and Indels. Before I can analyze it, I need to make sure the pipeline is suited for cancer genomics.
As for the pipeline, I've used BWA for alignment and GATK's Unified Genotyper for mutation calling. I understand that this method is appropriate for non-cancer sample analysis, as commented in Nature Review: http://www.nature.com/nrg/journal/v1...l/nrg2841.html
My problem comes from needing to call the somatic genome alteration detected in tumour and not detected in the normal data, as a differential analysis. From GATK, I've taken a look at "SomaticIndelDetector" (http://www.broadinstitute.org/gsa/ga...torWalker.html), which seems to call Indel, but ignores all the other possible SNP mutations. Beyond this, I have not had luck in finding online sources for appropriate Cancer Genome SGS analysis with Tumour-Normal paired analysis.
Can I ask those who have insight regarding to this matter for the advices and latest tools that I can use? Thanks in advance.
Regards,
CJ
As for the pipeline, I've used BWA for alignment and GATK's Unified Genotyper for mutation calling. I understand that this method is appropriate for non-cancer sample analysis, as commented in Nature Review: http://www.nature.com/nrg/journal/v1...l/nrg2841.html
My problem comes from needing to call the somatic genome alteration detected in tumour and not detected in the normal data, as a differential analysis. From GATK, I've taken a look at "SomaticIndelDetector" (http://www.broadinstitute.org/gsa/ga...torWalker.html), which seems to call Indel, but ignores all the other possible SNP mutations. Beyond this, I have not had luck in finding online sources for appropriate Cancer Genome SGS analysis with Tumour-Normal paired analysis.
Can I ask those who have insight regarding to this matter for the advices and latest tools that I can use? Thanks in advance.
Regards,
CJ
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