This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Finding mutations from bam files

I have two bam files(~17GB) for both tumor and normal sample in case of pancreatic cancer. Now I want to find the mutations in the tumor sample. How do I do that? Should I check the variants for tumor vs normal sample, or tumor vs reference genome(hg19). Pleas excuse my ignorance as I am relatively new to the field and still has got a lot to catch up. Thanks

next-gen sequencing
• 4,965 views • link
updated by MAPK MAPK • written by Gene_MMP8 Gene_MMP8

2 answers

Have a look at the GATK best practices for somatic mutations as a (good) starting point

• 0 views • link
written by WouterDeCoster WouterDeCoster

Thanks for the link. Can you suggest some command line tools?

• 0 views • link
written by Gene_MMP8 Gene_MMP8

First read the pages, then ask again. The tools from the best practices are command line tools.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Yes, the first thing you would want to do is create a VCF file using GATK tools as WouterDeCoster has mentioned. You can then use different analyses to call for variants that are statistically significant from your normal sample (so you will be comaparing tumour vs normal samples). If you have many unrelated normal samples to compare with, you could also adopt statistical approaches to find mutations in your samples. Reading this paper could give you some insight: http://www.nejm.org/doi/full/10.1056/NEJMoa1301689#t=article

• 0 views • link
written by MAPK MAPK
  1. SO first I am comparing reference vs tumor and creating the vcf file? and then tumor vs normal to call variants?
  2. Just to clarify, when you say, "if you have many unrelated normal samples to compare with", what do you mean? I have only two bam files normal and tumor taken from a single patient. By sample do you mean different patients? Or different sites of the body?
• 0 views • link
written by Gene_MMP8 Gene_MMP8

If you already have bam files, then use GATK protocol to create VCF file. Then do tumour vs normal comparison.

2. Just to clarify, when you say, "if you have many unrelated normal samples to compare with", what do you mean? I have only two bam files normal and tumor taken from a single patient. By sample do you mean different patients? Or different sites of the body?

You don't have an option to work with other statistical tests such as burden and SKAT test since you only have two samples.

• 0 views • link
written by MAPK MAPK

Thanks a lot for clearing that out. Really appreciate it.

• 0 views • link
written by Gene_MMP8 Gene_MMP8

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

• 0 views • link
written by WouterDeCoster WouterDeCoster

Log in to answer this question.

More posts like this