Compare two VCF files in Python

Question

[vpsev3]

Hello,

I would like to compare two VCF files in python

Here is my files : mygenome.csv and clinvar.csv

This is how I structured it, the two files are organized the same way, except that there is no "INFO" column in mygenome.vcf

I would like to find the identical rows in the POS column, then have the results in CSV with the POS, REF, ALT and INFO column

I searched for scripts but I have memory errors because the files are too large and I might lose data if I split them into several parts

[Renesh]

You can try the VCF file reader in Python as described here . Once you parse the files, you can compare them as you want.

[vpsev3]

It doesn't work

Does anyone have a solution?

[Ram]

It doesn't work

This is not sufficient description of failure. Show us sample data, expected results, actual results and the difference.

Answer 1

[Jorge Amigo]

If the data is really structured as you say so, this code should work:

perl -lane 'BEGIN {
open IN, "clinvar.csv" or die $!;
while (<IN>) {
 chomp; @cols = split "\t";
 $clinvar{ join "\t", @cols[0..2] } = $cols[3];
} close IN }
$index = join "\t", @F[0..2];
print "$index\t$clinvar{$index}" if exists $clinvar{$index}:
' mygenome.vcf

It stores clinvar information indexed by the first 3 columns, and it only prints the mygenome.vcf lines if clinvar annotation exists for that first 3 columns... except that then mygenome.vcf won't be really a vcf file.

What I would really do? Put your input.vcf file (proper vcf format) next to a clinvar.vcf file (proper vcf format) and use bcftools annotate.