Question: Is there a way to know which variant caller has been used for calling variants in TCGA?
1
gravatar for Jordan
5.5 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

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!

pipeline tcga variant-calling • 1.5k views
ADD COMMENTlink modified 5.5 years ago by Charles Warden7.3k • written 5.5 years ago by Jordan1.1k
1
gravatar for Charles Warden
5.5 years ago by
Charles Warden7.3k
Duarte, CA
Charles Warden7.3k wrote:

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/ 

ADD COMMENTlink written 5.5 years ago by Charles Warden7.3k

Thanks. I sent them a mail.

ADD REPLYlink written 5.5 years ago by Jordan1.1k

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

ADD REPLYlink written 3.9 years ago by jan120
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