Mutec2 - Liquid Biopsy

manolis

May 08, 2020 11:08

Can you please provide
a) GATK version used

v4130, v4160
b) Exact GATK commands used
c) The entire error log if applicable.

Dear team,

I want to use Mutect2 to call somatic mutations from cfDNA samples.

I found this post as also this (special use cases) and I would like to know if there are more details about how to set up Mutect2. Is there any special handle or set up or any recommendation in this case? I want to use it with Illumina NGS data, hot spot panel.

Many thanks

9 comments

Bhanu Gandham

May 24, 2020 09:34
Hi manolis

We are working on making the Mutect2 Liquid Biopsy pipeline available but its work under progress. We are unable to provide a timeline for its completion at the moment.
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manolis

May 25, 2020 07:47
Hi Bhanu Gandham,

I'm waiting for it in the future :)

Thanks!
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Bidossessi Wilfried Hounkpe

December 03, 2020 04:39
Dear Team,

I would like to know if the Mutect2 Liquid Biopsy pipeline is already available.

Thanks,
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Genevieve Brandt (she/her)

December 04, 2020 16:40
It is not yet available, it will be found here once it is.
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Bidossessi Hounkpe

December 12, 2020 22:48
Thanks.
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Kate Megquier

March 24, 2021 19:42
Hello,

I was wondering whether there are any updates on the Mutect2 pipeline for liquid biopsy?

Best,

Kate
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Genevieve Brandt (she/her)

April 09, 2021 19:08

Edited
Hi Kate,

We still do not have an expected date because our developer team had items come up that needed to be addressed first. We are continuing to work on it though and I'll update this post once it is released.

Genevieve
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yingchen69

April 21, 2022 02:10
Hi,

Is there any update on the Mutect2 pipeline for liquid biopsy or even the CLIA-approved liquid biopsy pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360055062832-New-Year-update-GATK-takes-on-2021)?

Best,

Ying
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sultan alharbi

October 16, 2022 16:06
Hi Great Team!!

Is there any update on the Mutect2 pipeline for liquid biopsy?
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