Is there a way to know which variant caller has been used for calling variants in TCGA?

Question

[Jordan]

Hi,

I have protected vcf's of TCGA cancers with me. I wanted to know which variant callers were used to generate them. I looked at the header of the vcf file to find it. There is a row in the header which says:

##vc_pipeline=bambam

So is this the variant caller? Or is this a pipeline? I have never heard of the bambam variant caller before. And neither could I find a pipeline called bambam.

Does anyone know?

Thanks!

Answer 1

[Charles Warden]

You might want to ask TCGA support ([e-mail] and/or [e-mail]) about this one: I know the same strategy isn't universally applied. For example, endometrial cancer has two MAF files from different sequencing centers: https://tcga-data.nci.nih.gov/docs/publications/ucec_2013/

[Jordan]

Thanks. I sent them a mail.

[jan]

Did you get a reply ? Can you share the answer ?