Mutect can't handle BAM files with multiple date information

sjanssen2 / spike

NGS pipeline for SNV detection in tumor context

BSD 3-Clause "New" or "Revised" License

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Mutect can't handle BAM files with multiple date information #110

Open sjanssen2 opened 6 years ago

sjanssen2 commented 6 years ago

##### ERROR @RG ID:160218_SN737_0377_BC8P60ACXX and 160315_SN737_0379_AC8NBPACXX and 150807_SN737_0363_AC7CKYACXX   CN:Department_of_Pediatric_Oncology_Dusseldorf  PU:C8P60ACXX and C8NBPACXX and C7CKYACXX    DT:2016/02/08 and 2016/03/05 and 2015/08/07 PL:ILLUMINA LB:SureSelectXTV5plusUTRautomated   SM:KB0006_c; File /gpfs/project/projects/spike/Intermediate/085_gatk_PrintReads/Keimbahn/KB0006_c.reCal.reAl.nodup.srt.bam; Line number 26

sjanssen2 commented 6 years ago

looks like we need to integrate multiple ReadGroups into printRead's bam files --> recompute a lot :-/