Compare two VCF files in Python

Compare two VCF files in Python

0

Hello,

I would like to compare two VCF files in python

Here is my files : mygenome.csv and clinvar.csv enter image description here

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


python

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