David Baux vidboda

## bed2intervals.awk
BEGIN {OFS=""} {if ($1 !~ /track/) {print $1,":",$2+1,"-",$3}}
#one-liner:
#awk 'BEGIN {OFS=""} {if ($1 !~ /track/) {print $1,":",$2+1,"-",$3}}' file.bed > file.list

## intervals2bed.awk
BEGIN { FS="[:-]";OFS="\t"} {print $1,$2-1,$3}
#one-liner:
#awk 'BEGIN { FS="[:-]";OFS="\t"} {print $1,$2-1,$3}' file.list > file.bed

## change_file_name.sh
#adapted from https://github.com/Char-Al/Miscellaneous
for i in *.tsv; do NAME=$( perl -pe 's/^(\w+)\.tsv$/$1_coverage.tsv/g' <<< $i);mv $i $NAME;done;

## addchr2vcf.sh
zcat file1.vcf.gz | awk -F"\t" '{if ($0 !~ /^#/) {print "chr"$0} else{print $0}}' | bgzip -c >file1chr.vcf.gz

## bedSize.sh
awk '{if (/^chr/){n+=$3-$2+1}}END{print n}' ROI.bed
	BEGIN {OFS=""} {if ($1 !~ /track/) {print $1,":",$2+1,"-",$3}}
	#one-liner:
	#awk 'BEGIN {OFS=""} {if ($1 !~ /track/) {print $1,":",$2+1,"-",$3}}' file.bed > file.list
	BEGIN { FS="[:-]";OFS="\t"} {print $1,$2-1,$3}
	#one-liner:
	#awk 'BEGIN { FS="[:-]";OFS="\t"} {print $1,$2-1,$3}' file.list > file.bed
	#adapted from https://github.com/Char-Al/Miscellaneous
	for i in *.tsv; do NAME=$( perl -pe 's/^(\w+)\.tsv$/$1_coverage.tsv/g' <<< $i);mv $i $NAME;done;