create BED file from whole genome index file

Question

[Ranold Grijon]

Dear altruists,

I found the below code online to create the bed file from whole genome indexed file. But I don't understand the code. Can anyone help me to crack this code?

awk -v FS="\t" -v OFS="\t" '{print $1 FS "0" FS ($2-1)}' GRCh38.primary_assembly.genome.fa.fai > GRCh38.primary_assembly.genome.bed

Answer 1

[Pierre Lindenbaum]

the fai file is a tab delimited file where the two first columns are

• chromosome name
• chromosome size

awk the command line

• -v FS="\t" defines a variable named FS as tab. FS is the input column delimiter for AWK. The first item/column for the current line will be $1, the second will be $2 etc...

• -v OFS="\t" defines a variable named OFS as tab. OFS is the out column delimiter for AWK

• {...} for each line in the input file, apply the following statements

• print $1 FS "0" FS ($2-1) : print "the first column of the current line, FS=the separator, the first base of the bed file which is 0, again FS, and then the value of the second column (the size of the chromosome minus 1)

your code is WRONG. You shouldn't substract 1 from the size, FS ad OFS shouldn't be specified that way.

a better way.

awk -F '\t' '{printf("%s\t0\t%s\n",$1,$2);}' in.fai