inst/guides/Guide.to.generating.catalogs.md

In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

Table of contents

• Introduction
• Input
• Test and example data
• Select the reference genome
• Select the genomic region
• Select the variant caller
• Optionally rename the samples
• Select and upload one or more VCFs
• Create the spectra catalogs
• Examine the spectra
• Signature attribution

Guide to generating spectrum catalogs and plots from VCFs in the mSigAct web server

Introduction

The function of the tab “Generate spectrum catalogs from VCFs” is, to generate spectrum catalogs from VCFs and also to plot the spectra.

The input area for uploading VCFs

Test and example data

These buttons provide some pre-loaded example data and several test VCFs that you can download and then re-upload.

Select the reference genome

Select the genomic region

Select the variant caller

Optionally rename the samples

Select and upload one or more VCFs

VCF formats are only partly standardized; please contact us if mSigAct has difficulty analyzing your VCF.

After the upload is complete, create the spectra catalogs

Once the catalogs are created, optionally examine the spectra

SBS96 and SBS192 spectra

SBS1536 and DBS79 spectra

DBS136 spectrum

Simplified DBS144 spectrum and indel spectrum

You can go to signature attribution any time after the catalogs are created

steverozen/mSigAct.server documentation built on July 9, 2023, 4:52 a.m.