Question: How to specify pipelines(muse, mutect,...) in TCGAbiolinks when you want to use hg19?
0
gravatar for nazaninhoseinkhan
3 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan400 wrote:

Dear all,

I am trying to use different mutation analysis pipelines(muse, mutect for my tumor samples using TCGABiolinks package. I want to use hg19 as the reference genome.

However it seems that I can only specify the certain pipeline using "pipeline="muse" in "GDCquery_maf()" which is used when our reference is hg38.

For hg19, GDCquery() function is used, but it is not clear which pipeline is used and how we can specify our desired pipeline.

I am looking forward to your comments

Nazanin

ADD COMMENTlink written 3 months ago by nazaninhoseinkhan400
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1634 users visited in the last hour