Description of the bug
Hi Sarek team,
Thanks for maintaining the workflow!
I think I may have encountered another bug. It looks like the paths to the filtered and normalized Mutect2 and Strelka VCF files in the samplesheet automatically generated by the variant-calling step may be incorrect. The filtered and normalized VCF files are stored under: /sarek/sarek_test/output/full_run/variant_calling/normalized, rather than within the corresponding mutect2 or strelka directories.
After manually correcting the paths in the sample sheet, the annotation step completed successfully.
samplesheet generated by the variant calling step:
patient,sample,variantcaller,vcf
PT01,PT01-T1_vs_PT01-5675-N,consensus,/sarek/sarek_test/output/full_run/variant_calling/consensus/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.consensus.vcf.gz
PT01,PT01-T1_vs_PT01-5675-N,manta,/sarek/sarek_test/output/full_run/variant_calling/manta/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.manta.diploid_sv.vcf.gz
PT01,PT01-T1_vs_PT01-5675-N,manta,/sarek/sarek_test/output/full_run/variant_calling/manta/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.manta.somatic_sv.vcf.gz
PT01,PT01-T1_vs_PT01-5675-N,mutect2,/sarek/sarek_test/output/full_run/variant_calling/mutect2/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.mutect2.filtered.bcftools_filtered.norm.sorted.vcf.gz
PT01,PT01-T1_vs_PT01-5675-N,strelka,/sarek/sarek_test/output/full_run/variant_calling/strelka/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.strelka.somatic_indels.bcftools_filtered.norm.sorted.vcf.gz
PT01,PT01-T1_vs_PT01-5675-N,strelka,/sarek/sarek_test/output/full_run/variant_calling/strelka/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.strelka.somatic_snvs.bcftools_filtered.norm.sorted.vcf.gz
PT01,PT01-T1_vs_PT01-5675-N,tiddit,/sarek/sarek_test/output/full_run/variant_calling/tiddit/PT01-T1_vs_PT01-5675-N/PT01-T1_vs_PT01-5675-N.tiddit_sv_merge.vcf.gz
Command used and terminal output
Relevant files
No response
System information
No response
Description of the bug
Hi Sarek team,
Thanks for maintaining the workflow!
I think I may have encountered another bug. It looks like the paths to the filtered and normalized Mutect2 and Strelka VCF files in the samplesheet automatically generated by the variant-calling step may be incorrect. The filtered and normalized VCF files are stored under:
/sarek/sarek_test/output/full_run/variant_calling/normalized, rather than within the correspondingmutect2orstrelkadirectories.After manually correcting the paths in the sample sheet, the annotation step completed successfully.
samplesheet generated by the variant calling step:
Command used and terminal output
Relevant files
No response
System information
No response