Which is @RG read group in the head of bam files?

Question

[Dan]

I am not sure which part of the head of bam files is @RG read group. I am curious why all of my samples have the same
A01494:44:H53Y7DMXY:1 part? Are they read groups?

samtools view -S Sample_7R-MDV_IGO_09530_H_1_dedup.bam | head -1  | awk '{print $1}'
A01494:44:H53Y7DMXY:1:2301:27579:4883
samtools view -S Sample_ST121_IGO_09530_H_7_dedup.bam | head -1  | awk '{print $1}'
A01494:44:H53Y7DMXY:1:2455:11785:2895
samtools view -S Sample_12L-8_IGO_09530_H_6_dedup.bam | head -1  | awk '{print $1}'
A01494:44:H53Y7DMXY:1:1249:11216:24111
samtools view -S Sample_7R-5_IGO_09530_H_3_dedup.bam | head -1  | awk '{print $1}'
A01494:44:H53Y7DMXY:1:1211:16559:28980
samtools view -S Sample_8L-5_IGO_09530_H_4_dedup.bam | head -1  | awk '{print $1}'
A01494:44:H53Y7DMXY:1:2340:30156:15984

Thanks Dan

Answer 1

[ATpoint]

What you are printing is the sequence identifier: https://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers

Read groups are stored in the header line starting with @RG, see:

https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups

Read Group In Sam/Bam Files: What Do They Exactly Describe?

How to get read group information for bam file

[Dan]

Hi,

I am using Picard to analyze whole-exome data, I have to add ReadGroups, what should I add for the RGID and RGPU? Can I add the sequence identifier?

java -jar ~/picard.jar AddOrReplaceReadGroups I=H_5_dedup.bam O=H_5_dedup.RG.bam RGID=A01494.44 RGLB=lib RGPL=illumina RGSM=H_5 RGPU=A01494.44.H53Y7DMXY.1

Thanks a lot!

Best Dan