How to keep only first part of the name when adding AddOrReplaceReadGroups in multiple BAM files at a time?

Question

[kabir.deb]

Hi,

I was wondering how can I use AddOrReplaceReadGroups for assinging Read Group (RG) tags for multiple bam files. I've 20 BAM files with names cfR_1....20_valAligned_star_mrdup_sort.bam generated using STAR aligner. Here, I'm expecting the added RG name should be only cfR_1, not the additional portion of the name.

cd /path to BAM/rnaBAM

file1=$(ls *_valAligned_star_mrdup_sort.bam | sed -n ${SLURM_ARRAY_TASK_ID}p)

picard AddOrReplaceReadGroups VALIDATION_STRINGENCY=LENIENT I=$file1 O=${file1%%.*}_rg.bam RGID=${file1%%.*} RGLB=${file1%%.*}
RGPL=illumina RGPU=run RGSM=${file1%%.*}


samtools view -H cfR_1_valAligned_star_mrdup_sort_rg.bam | grep "@RG"
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated.
@RG ID:cfR_1_valAligned_star_mrdup_sort LB:cfR_1_valAligned_star_mrdup_sort PL:illumina SM:cfR_1_valAligned_star_mrdup_sort PU:run

I ended up with ID:cfR_1_valAligned_star_mrdup_sort, while I just want cfR_1 to be mentioned only.

Answer 1

[kabir.deb]

Well, I got a solution, First I changed the input bam file name cfR_1_valAligned_star_mrdup_sort.bam to cfR-1_valAligned_star_mrdup_sort.bam, and then AddOrReplaceReadGroups.

picard AddOrReplaceReadGroups VALIDATION_STRINGENCY=LENIENT I=$file1 O=${file1%%.*}_rg.bam RGID=${file1%%_*} RGLB=${file1%%_*}
RGPL=illumina RGPU=run RGSM=${file1%%_*}