The frontline support team will be unavailable to answer questions on April 15th and 17th 2019. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

keeping read group information from a BAM file after remapping?

vakulmohantyvakulmohanty Cincinnati OhioMember


I'm trying to run GATK starting from a bam file with multiple read groups. I convert the bam file to interleveled fastq and realign it using BWA MEM. However neither BWA nor Picard to my knowledge allow me to reassign multiple readgroups. Would I be right to first split the original bam file by read groups, carry out alignment of the split bam files, convert them to fastq and then merge then with samtools merge so that all the read group information from the original bam file is captured in the realigned bam file?

I will be grateful for your comments and alternative methods and advice.

Thanking you,

Best Answer


Sign In or Register to comment.