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

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!

tcga pipeline variant-calling
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updated by Ram Ram • written by Jordan Jordan

1 answer

You might want to ask TCGA support (tcga@mail.nih.gov and/or tcga-dcc-binf-l@list.nih.gov) 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/

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updated by Ram Ram • written by Charles Warden Charles Warden

Thanks. I sent them a mail.

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written by Jordan Jordan

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

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written by jan jan

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