Novogene somatic results with GATK mutect2
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7 weeks ago
chrisgr ▴ 20

I was playing around with somatic data from Novogene. For one tumor-normal sample they provided a VCF file that contained about 100 somatic mutations. In their manual they state that they used GATK mutect2.

In order for me to understand what is going on I wanted to reproduce these somatic mutations using the tumor- and normal bam files. I howerver discovered ~13.000. I can't find anywhere what filtering methods they used. I've looked in their provided documentation but it only says it's been 'filtered'. What are common ways to filter somatic VCF files?

Thanks in advance!

Mutect2 Novogene GATK somatic VCF • 192 views
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Did you look in the header of the provided VCF to see if any information has been encoded there (e.g. command line/options used).

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