Assignment of Read group for Ion Torrent reads

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加藤啓輔

• June 08, 2020 15:51

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

Dear Community Forum,

I am Keisuke Kato working in Ibaraki Children's Hospital, Japan. I will ask you for the first time. I am creating a library using Thermo Fisher's Ion Ampliseq and doing exome analysis using Ion Proton. I am about to start the analysis with GATK 4.1.7.0. Simple BWA MEM command without assignment of @RG worked well in my PC. However, specification of @RG does not work. How should I specify the read group fields when mapping with BWA? Could you please tell me how to specify @RG BWA mapping commands, particularly, of PU, PL and LB for reads obtained with Ampliseq of Ion Proton? I would express my thanks for your support in advance.

Can you please provide
a) GATK version used：GATK 4.1.7.0.　 
b) Exact GATK commands used:

bwa mem -t 12 -M -R "@RG¥tID:842365DSAMKLCR¥tSM:842365DSAMKLCR¥tPL:IonProton"  GRCh38 842365DSAMKLCRFASTPcleanedcorrected.fastq > 842365DSAMKLCRFASTPcleanedcorrected.samc)entire error log if applicable.

[E::bwa_set_rg] no ID within the read group line

 

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• 

  Genevieve Brandt (she/her)

  • July 01, 2020 18:19

  We have created documentation on how to use read groups, here are some that will help you with this problem. 

  1) Read group documentation

  2) Errors about read group information

  3) AddOrReplaceReadGroups tool documentation. This can take a bam file and add read group information.

  Hopefully these will help you solve this issue.

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