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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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No read groups in bam #234

Open zoeward-nz opened 1 year ago

zoeward-nz commented 1 year ago

I'm trying to use bamstats04 or bamstats05. I downloaded the jar file from https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH

I tried running bamstats04 but it couldn't find it [SEVERE][JvarkitCentral]jvarkit command "bamstats04" not found so I ran bamstats05 instead: java -jar jvarkit.jar bamstats05 -B my.bed my.bam

I get: [SEVERE][BamStats05]No read groups in my.bam

I was given a paired fastq to analyse which I suspect has been run over separate lanes and concatenated before being given to me.

lindenb commented 1 year ago

I tried running bamstats04 but it couldn't find it

yes it's still a standalone program. I'll add to the main jvarkit in the next release.

No read groups in my.bam

your bam is missing read groups. https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups