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Old 02-10-2020, 04:13 AM   #1
bhumika
Junior Member
 
Location: Madrid, Spain

Join Date: Oct 2016
Posts: 1
Smile Convert vcf to bed based on PS field

Hello,
I want to convert the VCF file with phase information into a phase block bed format.
So if this is the file:

#CHROM POS REF ALT GT PS
Chr_1 1223 A G 1|0 1223
Chr_1 1245 A G 1|0 1223
Chr_1 1297 A G 1|0 1223
Chr_1 1450 A G 1|0 1450
Chr_1 1498 A G 1|0 1450

I wish to obtain a file like:

#CHROM START END
Chr_1 1223 1297
Chr_1 1450 1498

Please help!
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awk, bed, sed, shell-script, vcf file

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