Hi there!
My ultimate goal is to run GATK4.1.9.0 HaplotypeCaller on some BAM files. I used this code:
(base) Juliannes-MacBook-Pro:gatk-4.1.9.0 julianneradford$ ./gatk HaplotypeCaller \
> -R Rflav_transcriptome_sequences.fa \
> -I SRR5341585.bam \
> -O 85variants.g.vcf \
> -ERC GVCF
And even though the BAM file is a single sample, I get the error:
A USER ERROR has occurred: Argument emit-ref-confidence has a bad value: Can only be used in single sample mode enter code here currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file.
So, to try and figure out the Read Group name of my BAM file, I used the GATK recommended code:
(base) Juliannes-MacBook-Pro:samtools-1.11 julianneradford$ view -H /Applications/CompSci/gatk-4.1.9.0/SRR5341585.bam | grep '^@RG'
But this returns the error:
E26: Hebrew cannot be used: Not enabled at compile time
Does anyone know what this error means / how I can fix it? I cannot find anything related to it online. Thanks, Julie
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julianneradford •
samtools view
not
view
Hello! Thanks for your reply. However, when I use
samtools view
I get this error:
samtools: command not found
I (think) I have followed all instructions to properly install samtools, add it to the path, and am making sure I am working in the right directory so I am not sure why this happens.
echo ${PATH} | tr ":" "\n" | xargs ls | grep samtools
if empty, there is something wrong with your PATH.
Okay I see. I checked that and it says for all of the directories I've added "no such file or directory" Clearly I must not be adding things to my PATH correctly then. I have been added the following directories to my PATH in this way:
export PATH="$/Applications/Python\ 2.7/:$PATH"
export PATH="$/Users/julianneradford/miniconda3/:$PATH"
export PATH="$/Applications/CompSci/gatk-4.1.9.0/samtools-1.11/:$PATH"
export PATH="$/Applications/CompSci/gatk-4.1.9.0/:$PATH"
I appreciate your help and let me know if there is something I can fix here. Thanks.
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