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Old 10-09-2013, 04:34 AM   #18
Location: Milan

Join Date: May 2013
Posts: 40


I guess then I can use the option of TableRecalibration, I am yet to run it , if it produces a bam file good enough else I will use the print read option which will surely produce a bam file. As for multiple sample with merged bam file, I will be getting my samples say (4 samples are sequenced in one lane) then I guess I might have to use the merged bam file concept or might simply work with individual samples and during the unified genotyper I can use all of them together (what do you think). My sample for project will be 2 Tumor and 2 IPSC from the same 2 tumors. So it is 2 tumors from 2 different patients and their respective IPSC lines and I will try to work it out to find the SNP INDELs SNVs that will confer that the mutations between tumor and IPSC are same so that they have same genetic background but then in that case during the SNP INDEL calling using unified genotyper is it advisable to use all the recaliberated bam files from 4 samples to call together and get the SNP and INDELS right? Any thoughts on this?

Bedfile query:
This is what I was worried about regarding the bed file, as for the test analysis I am doing I can recreate a bed file myself from the genome browser for testing my analysis? Let me know your thoughts on this.
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