[vg giraffe] Unable to add read group to BAM file

Question

[saruman]

Hi everyone,

I am aligning short read sequences (HG002) against the Human pangenome reference graph using VG Giraffe. Specifically, I am using the .gbz and .hapl index files to generate the BAM file. The alignment works without issues; however, I am unable to add the read group (I can do it using Picard, though I would like to spare this additional step).

singularity exec \
    -B /fs/scratch/PAS2525/trimmed:/input \
    -B /fs/scratch/PAS2525/output:/output \
    -B /fs/scratch/PAS2525/References/hprc:/index \
    -B /fs/scratch/PAS2525/tmp:/tmp \
    /fs/scratch/PAS2525/Singularity/vg_v1.68.0.sif \
    vg giraffe \
    --progress --rescue-algorithm none --output-format bam --threads 44 \
    --read-group 'ID:1\tSM:HG002\tLB:lib1\tPL:illumina\tPU:unit1' \
    --gbz-name /index/hprc.gbz \
    --haplotype-name /index/hprc.hapl \
    --kff-name /output/HG002.kff \
    --fastq-in /input/HG002.NovaSeq.pcr-free.35x.trimmed_R1.fastq.gz \
    --fastq-in /input/HG002.NovaSeq.pcr-free.35x.trimmed_R2.fastq.gz \
    > /fs/scratch/PAS2525/HG002.bam

Does anyone know why I am unable to add the read group? I have also tried the following string without success:

--read-group '@RG\tID:1\tSM:HG002\tLB:lib1\tPL:illumina\tPU:unit1'

Thank you in advance for any help.

[Arup Ghosh]

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