Whenever you encounter an error, please also include:
[0.10.7] Version of PCGR.
[grch38] Genome build (grch37/grch38).
[singularity exec -e -B /share/app/PCGR/data-20220118:/data -B /path/to/outdir:/outdir -B /path/to/vcfdir:/vcfdir -B /path/to/cnadir:/cnadir /share/app/PCGR/pcgr-v0.10.7.sif /opt/mambaforge/envs/pcgr/bin/pcgr --pcgr_dir /data --genome_assembly grch38 --input_vcf /vcfdir/test.vcf.gz --sample_id test --output_dir /outdir --vep_regulatory --estimate_tmb --estimate_msi_status --estimate_signatures --tumor_dp_tag TDP --tumor_af_tag TVAF --control_dp_tag NDP --control_af_tag NVAF --call_conf_tag TAL --input_cna /cnadir/test.seg.tsv --tumor_site 9 --tumor_purity 0.37 --tumor_ploidy 3.3 --vcf2maf --show_noncoding --assay WGS --include_trials --force_overwrite --no_docker] the complete command you used to invoke pcgr (including all explicit options)
[2022-01-19 22:16:10 - pcgr-report-generation - INFO - Generating report data for copy number segment file /cnadir/test.seg.tsv
Error: Column intogen_drivers not found in .data] the full error message
Whenever possible, please also provide links to query VCF file.
Additional context
Add any other context about the problem here.
Whenever you encounter an error, please also include:
intogen_drivers
not found in.data
] the full error messageWhenever possible, please also provide links to query VCF file.
Additional context Add any other context about the problem here.