plotting AF in vcf files

Question

[rheab1230]

Hello everyone, I want to plot AF distribution for all my vcf files. Is there any software to do that. I tried using vcfstats but its showing error in my vcf files.

[rheab1230]

I got AF from vcf files using vcftools software. Now I am trying to plot these values using the command:

plot(density(var_qual$X.FREQ.))
Error in density.default(var_qual$X.FREQ.) : argument 'x' must be numeric

The thing is that in my case I have two frequency value being available at one position.

22 chr
51238249 pos
2 alleles
930  N_CHR
0.910753    0.0892473 freq

[Kevin Blighe]

Hi, what is the output of str(var_qual)?

I would use bcftools query to output the AF values, and then import these to R where I would plot them via plot(), density(), and/or hist()

[rheab1230]

This is the output of str(var_qual)

data.frame':    1 obs. of  6 variables:
 $ X.cichlid_subset.: chr "cichlid_subset"
 $ X.CHROM.         : chr "CHROM"
 $ X.POS.           : chr "POS"
 $ X.N_ALLELES.     : chr "N_ALLELES"
 $ X.N_CHR.         : chr "N_CHR"
 $ X..FREQ..        : chr "{FREQ}"

Answer 1

[sbstevenlee]

Here is a Python API solution using the pyvcf.VcfFrame.plot_hist method I wrote.

Below is a simple example:

from fuc import common, pyvcf
common.load_dataset('pyvcf')
vcf_file = '~/fuc-data/pyvcf/normal-tumor.vcf'
vf = pyvcf.VcfFrame.from_file(vcf_file)
vf.plot_hist('DP')

We can draw multiple histograms with hue mapping:

annot_file = '~/fuc-data/pyvcf/normal-tumor-annot.tsv'
af = common.AnnFrame.from_file(annot_file, sample_col='Sample')
vf.plot_hist('DP', af=af, group_col='Tissue')

We can show AF instead of DP:

vf.plot_hist('AF')

[rheab1230]

Thank you so much for this. I will definitely try this.

[rheab1230]

Hello, I am using the command to plot AF distribution for vcf files. But I am getting some error. The command:

#!/bin/python
from fuc import common, pyvcf
common.load_dataset('pyvcf')
vcf_file = 'GEUVADIS.chr22.genotype.vcf'
vf = pyvcf.VcfFrame.from_file(vcf_file)
vf.plot_hist('AF')

the error:

file.python:5: DtypeWarning: Columns (5) have mixed types.Specify dtype option on import or set low_memory=False.
vf = pyvcf.VcfFrame.from_file(vcf_file)
Traceback (most recent call last):
File "file.python", line 6, in
vf.plot_hist('AF')
File "/home/anaconda3/envs/var/lib/python3.7/site-packages/fuc/api/pyvcf.py", line 1991, in plot_hist
df = self.extract(k, as_nan=True, func=d[k])
File "/home/anaconda3/envs/var/lib/python3.7/site-packages/fuc/api/pyvcf.py", line 3912, in extract
df = self.df.apply(one_row, axis=1)
File "/home/anaconda3/envs/var/lib/python3.7/site-packages/pandas/core/frame.py", line 8736, in apply
return op.apply()
File "/home/anaconda3/envs/var/lib/python3.7/site-packages/pandas/core/apply.py", line 688, in apply
return self.apply_standard()
File "/home/anaconda3/envs/var/lib/python3.7/site-packages/pandas/core/apply.py", line 805, in apply_standard
results, res_index = self.apply_series_generator()
File "/home/anaconda3/envs/var/lib/python3.7/site-packages/pandas/core/apply.py", line 821, in apply_series_generator
results[i] = self.f(v)
File "/home//anaconda3/envs/var/lib/python3.7/site-packages/fuc/api/pyvcf.py", line 3901, in one_row
i = r.FORMAT.split(':').index(k)
ValueError: 'AF' is not in list

[sbstevenlee]

I responded to your GitHub issue here: https://github.com/sbslee/fuc/issues/39

[rheab1230]

Yes, I saw that. Thank you.

Answer 2

[Pierre Lindenbaum]

I want to plot AF distribution for all my vcf files. Is there any software to do that.

 bcftools stats --af-bins 0.1,0.2,0.3,0.5,1.0 input.vcf

followed by

plot-vcfstats

http://samtools.github.io/bcftools/bcftools.html#plot-vcfstats

[rheab1230]

Okay, I will do that. Thank You.

Answer 3

[cocchi.e89]

Take a look at this: plot-VCF

It allows you to graphically visualize any flag (and much more) from your VCF file