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divide vcf file by consequence

I have a VEP annotated VCF file I want to divide it based on consequence, my approach is:

awk '{ gsub(",","-",$4); print $0 >> $4".txt"}' input.txt

I substitute "," by "-" so file naming be convenient, but as a result because I depend on column 4 for naming; also the resulted file will contains "-"

for example if column number 4 is
start_lost,splice_region_variant
The output file will be
start_lost-splice_region_variant.txt
Which what I want. However, the resulted data in the file will be
start_lost-splice_region_variant instead of start_lost,splice_region_variant which is incorrect.

Any suggestion?

vcf awk
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written by Medhat Medhat

Could you provide first few lines of the vcf? May be head file.vcf?

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written by venu venu

1 answer

do a copy of $0?

awk '{ P=$0; gsub(",","-",$4); print P >> $4".txt"}' input.txt
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written by Pierre Lindenbaum Pierre Lindenbaum

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