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bash add chr to beginning of vcf

Charles-Alexandre Roy answered on October 10, 2020 Popularity 1/10 Helpfulness 8/10

answer bash add chr to beginning of vcf

bash add chr to beginning of vcf

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# Example usage:
awk '{if($0 !~ /^#/) print "chr"$0; else print $0}' input.vcf
# This converts a vcf file with numeric genome coordinates to one with 
# chr in front of the chromosome number. 

# Note, this command does the opposite operation, if needed:
awk '{gsub(/^chr/,""); print}' input.vcf

Popularity 1/10 Helpfulness 8/10 Language shell

Source: www.biostars.org

Tags: add bash chr shell

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Contributed on Oct 10 2020

Charles-Alexandre Roy

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