add sample name to bam header based on bam file name

Question

[Ana]

I have a group of bam files but some of them do not have sample name SM in @RG,

example: sample1.gh37.bam

@RG     ID:13048        CN:BCCAGSC      LB:NA   PL:illumina     PU:NA   SM:N/A

I want to add the file name (but without "gh37.bam" suffix) to SM , to get something like this

@RG     ID:13048        CN:BCCAGSC      LB:NA   PL:illumina     PU:NA   SM:sample1

Any help how I can do it

Answer 1

[Pierre Lindenbaum]

picard AddOrReplaceReadGroups https://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups or samtools addreplacerg

[Ana]

for file in *.bam; do
base_name=$(basename $file .grch37.bam);
samtools addreplacerg -r "SM:${base_name}" -o ${base_name}.bam $file;
done

Already using this but I get The supplied RG line lacks an ID ta error

[Pierre Lindenbaum]

option -r "ID:xxxx" is required.

[Ana]

I do not want to change the ID, its the same. How can I adjust it?

[Pierre Lindenbaum]

http://www.htslib.org/doc/samtools-addreplacerg.html

-R STRING Allows you to specify the read group ID of an existing @RG line and applies it to the reads specified.