platypus variant calling region files #awk #commandline #ngs #variant caller #platypus

for target sequencing platypus variant caller needs a file with regions in a specific format:

chr1:100-200

awk allow to transform a bed file in this specific region format:

cat input.bed | awk 'BEGIN {OFS=""}; {print($1,":",$2,"-",$3)}'> regions.txt before:

chr1 36931685 36932519 CSF3R_NM_156039_exon_17 chr1 36932820 36932922 CSF3R_NM_156039_exon_16 chr1 36933148 36933262 CSF3R_NM_156039_exon_15 chr1 36933412 36933573 CSF3R_NM_156039_exon_14 chr1 36933665 36933832 CSF3R_NM_156039_exon_13 chr1 36934746 36934868 CSF3R_NM_156039_exon_12 chr1 36935242 36935451 CSF3R_NM_156039_exon_11 chr1 36937023 36937257 CSF3R_NM_156039_exon_10

after:

chr1:36931685-36932519 chr1:36932820-36932922 chr1:36933148-36933262 chr1:36933412-36933573 chr1:36933665-36933832 chr1:36934746-36934868 chr1:36935242-36935451