Loop to change a @RG in a BAM file

Question

[mwerseb1]

Hello,

I am trying to change the @RG from "ID:i" to "ID:MyFileName" in a number of files using a while read loop. My syntax is as follows:

ls *.sorted.bam|awk -F "." '{print $1}'| while read name; do
samtools view -H $name.sorted.bam| sed 's/ID:i/ID:$name/'|samtools reheader - $name.sorted.bam > $name.sorted_rh.bam;
done

Everything works perfectly except in the reheadered bam file the "ID:i" is replaced with "ID:$name" not the file name. Any ideas about how to fix this? When not in a loop the sed command changes the strings correctly.

Thanks

[finswimmer]

This should work as well:

samtools addreplacerg -r "ID:$name" -o $name.sorted_rh.bam $name.sorted.bam

Answer 1

[Pierre Lindenbaum]

use double quote instead of single quote

sed "s/ID:i/ID:$name/"

see https://stackoverflow.com/questions/6697753/difference-between-single-and-double-quotes-in-bash

[mwerseb1]

That seems to have worked! Thanks!