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Clinical-Genomics-Lund / nextflow_wgs

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Contamination for panels and wgs #238

Open ViktorHy opened 1 month ago

ViktorHy commented 1 month ago

For WGS run with full dataset. 

singularity exec --bind /fs1 /fs1/resources/containers/verifybamid2_2.0.1.sif \
     verifybamid2 \
    --SVDPrefix /fs1/resources/ref/hg38/VerifyBamID/resource/no_chr/1000g.phase3.100k.b38.vcf.gz.dat \
    --Reference /fs1/resources/ref/hg38/fasta/masked/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.fna \
    --BamFile $i

For panels, run with exome dataset and disable sanity check, otherwise some samples might crash.

singularity exec --bind /fs1 /fs1/resources/containers/verifybamid2_2.0.1.sif \
    verifybamid2 \
    --DisableSanityCheck \
    --SVDPrefix /fs1/resources/ref/hg38/VerifyBamID/resource/exome/no_chr/1000g.phase3.10k.b38.exome.vcf.gz.dat \
    --Reference /fs1/resources/ref/hg38/fasta/masked/GCA_000001405.15_GRCh38_no_alt_analysis_set_nochr.fna \
    --BamFile $i
ViktorHy commented 2 days ago

Further testing revealed some flaws for this approach using paneldata. I would suggest using our in-house script for now.