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ok so as it turns out, due to the csv coming from excel, my seperators look more like this:

"exonic","ALS",4567,112,44,text,"moretext","34","text,with,comma"

I got the code to work some of the...

That works for the exact files I gave you, but not for my actual files.

The main difference is that my actual files are bigger and the columns for the first file are in a different place - the...

I have two files (csv and vcf) which look exactly like this

S1.csv
func,gene,start,info
"exonic","AL","2309","het"
"exonic","NEF","6912","hom"S1.vcf
##fileinfo
#CHROM POS ID INFO
chr1 ...