New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Contamination for panels and wgs #238

Open

ViktorHy opened this issue Oct 2, 2024 · 1 comment

Assignees

Collaborator

ViktorHy commented Oct 2, 2024 •

edited

Loading

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

The text was updated successfully, but these errors were encountered:

Jakob37 assigned A97paupic

Collaborator Author

ViktorHy commented Nov 12, 2024

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment