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GATK command for mutect2

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
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updated by vdauwera vdauwera • written by 1si17bt025 • 1si17bt025

Is there any particular tool to run mutect2??

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written by 1si17bt025 • 1si17bt025

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!!!

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written by 1si17bt025 • 1si17bt025

1 answer

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

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written by vdauwera vdauwera

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