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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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sort removing tags from @RG header #356

Closed Kurt-Hetrick closed 6 years ago

Kurt-Hetrick commented 6 years ago

Hello, when using sambamba sort on a bam file, i am finding that the PM tag for the RG header is being stripped out. I am using sambamba 0.6.7

bam file (brief particulars are that file is created with bwa mem 0.7.15 | samblaster | picard AddOrReplaceReadGroups | picard markduplicates {from querysort, v 2.17.0}) before sambamba sort

samtools view -H foo.dup.bam | grep ^@RG @RG ID:foo LB:foo PL:ILLUMINA SM:foo PU:foo CN:foo DT:2017-12-10T00:00:00-0500 PG:foo PM:HiSeq2500_HighOutput

then after running sambamba sort, the PM tag has been removed.

/mnt/research/tools/LINUX/SAMBAMBA/sambamba_v0.6.7/sambamba sort -o bar.bam foo.dup.bam

khetric1@c6100-9> samtools view -H bar.bam | grep ^@RG @RG ID:foo CN:CIDR DT:2017-12-10T00:00:00-0500 LB:foo PG:foo PL:ILLUMINA PU:foo SM:foo

I couldn't find this in open or closed issues.

Thanks in advance,

Kurt

pjotrp commented 6 years ago

Thanks for the report. I'll check it.