Question

GATK command for mutect2

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2.9 years ago

1si17bt025 • 0

I want to use GATK for somatic mutation prediction. I presently have a mapped BAM file from BWA. As I'm new to GATK I request someone to give me the commands to be used in GATK to get the VCF file. I had used the hg38 reference from NCBI for BWA. Thanks for the help.

Gatk command mutect2 • 1.5k views

ADD COMMENT • link updated 2.9 years ago by vdauwera ★ 1.2k • written 2.9 years ago by 1si17bt025 • 0

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I suspect you're the very same user that posted the same question a few hours ago : GATK commands for mutect2 ?

ADD REPLY • link 2.9 years ago by Pierre Lindenbaum 164k

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you can use this https://www.jianshu.com/p/a10876c7fd81

ADD REPLY • link 2.9 years ago by xiaoguang ▴ 160

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Is there any particular tool to run mutect2??

ADD REPLY • link 2.9 years ago by 1si17bt025 • 0

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I'm learning to get vcf file for somatic mutation. Could you please help me for getting vcf file.

I worked with HaplotypeCaller for germline varriant. Now want to work on somatic mutation prediction.

PLEASE HELP!!!

ADD REPLY • link 2.9 years ago by 1si17bt025 • 0

score 1 · Answer 1 · 2021-12-23

If you’re looking for an end-to-end explanation of the Mutect2 somatic analysis workflow, you may be interested in the O’Reilly book Genomics in the Cloud, which I coauthored. It explains a lot about how to run GATK and the Best Practices pipelines. (Despite the title, all the core explanations apply whether you run it locally, on a cluster or on the cloud)

https://oreil.ly/genomics-cloud