Checking ReadGroup name in BAM file with GATK instructions
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a) GATK version used:
b) Exact command used:
c) Entire error log:
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My ultimate goal is to run GATK4.1.9.0 HaplotypeCaller on some BAM files. In doing so I get an error saying I need to specify the read group name of the sample for the BAM file (it is a single sample). Using the GATK Read Groups page, I used a command to try and figure out the name of the read group and this is where I am having problems.
a) GATK version used: 4.1.9.0
b) Exact command used:
view -H /Applications/CompSci/gatk-4.1.9.0/SRR5341585.bam | grep '^@RG'
c) Entire error log:
E26: Hebrew cannot be used: Not enabled at compile time
Any help is appreciated, thanks!
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Hi Julianne Radford,
The command should be samtools view, for example:
samtools view -H sample.bam | grep '^@RG'
You can see more information on this page: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Best,
Genevieve
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