Mutational landscape plot from VCF files
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Entering edit mode
17 months ago

Hi there,

I am trying to find a program or code that will let me use VCF files generated from RNA-seq data (non-model organism) to create a mutational landscape plot (or rainfall plot). Any program recommendations?

Thanks.

gatk genome RNA-Seq R galaxy • 1.5k views
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3
Entering edit mode
17 months ago
sbstevenlee ▴ 480

Check out the pymaf.MafFrame.plot_oncoplot method I wrote:

from fuc import common, pymaf
common.load_dataset('tcga-laml')
f = '~/fuc-data/tcga-laml/tcga_laml.maf.gz'
mf = pymaf.MafFrame.from_file(f)
mf.plot_oncoplot()

enter image description here

You can convert VCF to MAF with the pymaf.MafFrame.from_vcf method:

from fuc import pymaf
mf = pymaf.MafFrame.from_vcf('annotated.vcf')
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0
Entering edit mode

interesting ! How do I read this kind of figure ? what is the x-axis ? what is 'TMB' ? ...

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Entering edit mode
17 months ago
sbstevenlee ▴ 480

Just wanted to let you know that you can now use the fuc package to draw a rainfall plot directly from VCF with the pyvcf.VcfFrame.plot_rainfall method:

enter image description here

import matplotlib.pyplot as plt
import seaborn as sns
from fuc import common, pyvcf
common.load_dataset('brca')
vcf_file = '~/fuc-data/brca/brca.vcf'
vf = pyvcf.VcfFrame.from_file(vcf_file)
vf.plot_rainfall('TCGA-A8-A08B',
                 figsize=(14, 7),
                 palette=sns.color_palette('Set2')[:6])
plt.tight_layout()
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0
Entering edit mode
7 days ago
cocchi.e89 ▴ 230

Take a look at this: plot-VCF

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