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
You can try the VCF file reader in Python as described here . Once you parse the files, you can compare them as you want.
It doesn't work
Does anyone have a solution?
This is not sufficient description of failure. Show us sample data, expected results, actual results and the difference.