AmpliconSeq - FASTQ files - Analysis Tools

[ravi]

Hi,

I have VCF files from cnvkit and mutect2. May I know if I could use any tools in GP for further downstream analysis to generate plots/figures generation?

Targeted/amplicon sequencing data is generated using FFPE tumour samples that includes:

n=8 - Untreated (4) and treated (4).

I would like to compare CNV and mutation plots between the untreated and treated samples.

Your expert suggestion will be very helpful.

Thank you,

Ravi.

[Michael Reich]

Hi Ravi,

Available downstream analyses from Mutect2 are MutSigCV and MutPanning - please take a look at these and see if they are suitable for your purposes. For visualization and creation of figures, I suggest the Integrative Genomics Viewer (IGV), which is available as a GenePattern module and in other formats at https://igv.org.

Best,
Michael

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Michael Reich
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University of California, San Diego
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[ravi velaga]

Thank you very much for the information, Michael. I will look into the documentation.

If you don't mind a quick follow up question, could you share your expert suggestion whether  VCFs from target sequencing after Mutect2 can be used as inputs for MutSigCV and MutPanning or if they are more reliable when WGS data is used ?

Best Regards,

Ravi.

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[Michael Reich]

Hi Ravi,

You can use VCF files, but since MutSigCV and MutPanning both require MAF files as inputs, you would need to convert your VCF files to MAF format. There are several tools available to do this, such as vcf2maf . 

Best,
Michael

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[ravi velaga]

Thank you, Michael.

Looks like the input MAFs are only from WGS or WES but not from Targeted Amplicon Seq.

Best Regards,

Ravi.

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