I have called SNP and INDEL in two matched samples by strelka and extract this information from .vcf file and I have these

1   928006  G   A   t_005
1   1649842 G   T   t_005
1   2020408 G   A   t_005
1   2031677 T   A   t_005


1   14115   A   T   o_005
1   541052  T   C   o_005
1   1088123 T   G   o_005
1   1232501 A   G   o_005

I need to show if and how extend the mutations between these two samples are consistent by a circos plot but really I don't know how people do that

Something like this

enter image description here


enter image description here

  • 2
    $\begingroup$ FWIW, I've never found a use case where a Circos plot was the best visualisation tool. They look pretty, but they don't really convey much information. $\endgroup$
    – Joe Healey
    Apr 1 '19 at 13:12
  • $\begingroup$ Thank you, I tried a waterfall to show the landscape of mutations in two samples but I failed again. I need a way to show which extend the mutations between these two samples are consistent $\endgroup$
    – Exhausted
    Apr 1 '19 at 13:16
  • 1
    $\begingroup$ Then you could use a confusion matrix, e.g. i66.tinypic.com/eanz9c.jpg $\endgroup$ Apr 1 '19 at 13:22
  • 1
    $\begingroup$ I've posted my suggestion as an answer to not clutter the comments here. $\endgroup$ Apr 1 '19 at 13:44
  • 1
    $\begingroup$ I agree that maybe a confusion matrix would be better, however there is a nice circos package in R github.com/jokergoo/circlize. You can use the spread function in dplyr to change the dataframe into a square matrix. $\endgroup$
    – TW93
    Apr 1 '19 at 14:26

A circos plot is most likely not the most appropriate solution here. What I would suggest is a confusion matrix, of which you can find an example here:

enter image description here

For every variant in your vcf you'll add a number in this matrix. One sample is the columns, the other is the lines. If your variant is homozygous in both, then you add in that square +1 (the cell with 5845 in the example).

A perfect concordant sample pair will have only variants on the diagonal.

Here is some python code to get such a matrix. It uses cyvcf2 and pandas, and expects as input a vcf file with both samples.

from argparse import ArgumentParser
from cyvcf2 import VCF
import pandas as pd

def main():
    args = get_args()

def confusion_matrix(vcff):
    First level of the dict is the "first" call, second level is the "second" sample
    0: hom_ref
    1: heterozygous
    2: unknown/nocall
    3: hom_alt
    zygosities = {0: {0: 0, 1: 0, 2: 0, 3: 0},
                  1: {0: 0, 1: 0, 2: 0, 3: 0},
                  2: {0: 0, 1: 0, 2: 0, 3: 0},
                  3: {0: 0, 1: 0, 2: 0, 3: 0},
    for v in VCF(vcff):
        zygosities[v.gt_types[0]][v.gt_types[1]] += 1
    zygs = [2, 0, 1, 3]
    df = pd.DataFrame(index=zygs, columns=zygs)
    for tr in zygs:
        for te in zygs:
            df.loc[tr, te] = zygosities[tr][te]
    df.columns = ['nocall', 'hom_ref', 'het', 'hom_alt']
    df.index = ['nocall', 'hom_ref', 'het', 'hom_alt']

def get_args():
    parser = ArgumentParser(description="Create confusion matrix of SNV calls")
    parser.add_argument("vcf", help="vcf containing two samples")
    return parser.parse_args()

if __name__ == '__main__':
  • $\begingroup$ Thank you, for example if I have filtered t_005.vcf anf o_005.vcf files in a directory, how this code locate them? $\endgroup$
    – Exhausted
    Apr 1 '19 at 13:46
  • $\begingroup$ It needs a single vcf with both samples. For that you'll need bcftools merge to combine your vcf files. $\endgroup$ Apr 1 '19 at 13:48

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