search

cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
57 stars 20 forks source link

Readgroup does not exist #90

Closed podro182 closed 4 years ago

podro182 commented 4 years ago

Hi there and thanks for the well though out method :)

I'm trying to run brass 6.0.0 (I created all the required files as per wiki instructions), however I'm encountering the following error: Readgroup 'A00559_78_HGMLJDRXX_3' does not exist.

I ran a sanity check with the picard tool ValidateSamFile and the BAM file seems ok. Plus the bam also plays well with other tools. I also checked that the readgroup is present in the header.

Do you have any suggestions on what might be wrong?

keiranmraine commented 4 years ago

This sounds like one of the following:

  1. The records in the BAM file have RG aux tags that are not found in the header as @RG records.
  2. Have you generated bas files using bam_stats?
podro182 commented 4 years ago

Thanks for the quick reply :)

  1. The RG that gives the error is present in the header (error: Readgroup 'A00559_78_HGMLJDRXX_3' does not exist): @RG ID:A00559_78_HGMLJDRXX_3 PL:ILLUMINA PU:A00559_78_HGMLJDRXX_3 LB:XXX-Tumor-WGS_TruSeqUDI_A00559_0078 SM:XXX-Tumor-WGS_TruSeqUDI_A00559_0078 CN:RH-GM

  2. Yes, bas was generated like that: bam_stats.pl -i $name'.bam' -o $name'.bam.bas'

keiranmraine commented 4 years ago

Can you confirm the *.bam.bas file contains A00559_78_HGMLJDRXX_3

podro182 commented 4 years ago

That's it, thanks a lot for the help! For some reason this readgroup is missing