"TOKENS_PON" is for WGS?

cbaocbao Member, Broadie ✭✭

Hi,

I want to analyze somation mutations in my own WGS data using Firecloud. I am a little bit confused about the ”TOKENS_PON” (as shown in the following) for Mutect filter. Based on “broad-mutation-calling-best-practice-workflows”, this PoNs comprise approximately 1000 carefully curated TCGA normals sequenced with Agilent. So, I just want to know whether this PoN includes whole genome regions and can be used in WGS mutect filtering. Since I have dbGAP account, is it better to build my own WGS PoN by TCGA blood normal sample for mutect filter? All suggestions are welcome.

TOKENS_PON gs://firecloud-tcga-dcc-closed-access/reference/PoNs/final_summed_tokens.hist.bin

Thank you very much!

Best,
Chunyang

Issue · Github
by Sheila

Issue Number
2474
State
closed
Last Updated
Assignee
Array
Milestone
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Closed By
sooheelee

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @cbao
    Hi Chunyang,

    Let me check with the team and get back to you.

    -Sheila

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    P.S. @cbao, it turns out the Cancer Genome Analysis (CGA) group who writes many of these methods can answer your question. I've moved this post to their subsection of the forum. Someone will followup with you shortly.

  • cbaocbao Member, Broadie ✭✭

    @shlee said:
    P.S. @cbao, it turns out the Cancer Genome Analysis (CGA) group who writes many of these methods can answer your question. I've moved this post to their subsection of the forum. Someone will followup with you shortly.

    Thank you so much! It's really helpful.

  • cbaocbao Member, Broadie ✭✭

    @Sheila said:
    @cbao
    Hi Chunyang,

    Let me check with the team and get back to you.

    -Sheila

    Thanks!

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