Closed alexcoppe closed 5 months ago
You will need to basecall your data with a consistent basecaller model. The variant calling models are unique to each basecaller, as such it is not possible to perform variant calling with a mixture of data from different basecallers.
Ok, but in the previous version, it worked with more than one variant calling model. I'll try using just one! Thank you.
Picked up again in https://github.com/epi2me-labs/wf-somatic-variation/issues/26
Operating System
Other Linux (please specify below)
Other Linux
Red Hat Enterprise Linux release 8.6
Workflow Version
v.1.2.1
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
/hpcshare/genomics/ASL_ONC/NextFlow_RunningDir/nextflow-23.10.0-all run epi2me-labs/wf-somatic-variation -profile singularity -resume -process.executor 'pbspro' -process.memory 256.GB -work-dir '/archive/s2/genomics/onco_nanopore/test/test' -with-timeline --snv --sv --sample_name 'OHU0002HI' --bam_normal '/archive/s2/genomics/onco_nanopore/HUM_OHU_OHU0002HTNDN/OHU0002HTNDN.bam' --bam_tumor '/archive/s2/genomics/onco_nanopore/HUM_OHU_OHU0002ITTDN/OHU0002ITTDN.bam' --ref '/archive/s1/sconsRequirements/databases/reference/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta' --out_dir '/archive/s2/genomics/onco_nanopore/test' --basecaller_cfg 'dna_r10.4.1_e8.2_400bps_sup@v4.2.0' --phase_normal --classify_insert --force_strand --normal_min_coverage 0 --tumor_min_coverage 0 --haplotype_filter_threads 32 --severus_threads 32 --dss_threads 4 --modkit_threads 32 -process.cpus 32 --mod
Workflow Execution - CLI Execution Profile
singularity
What happened?
Stopped working when reading the BAM generated by Dorado because reads basecalled with more than one basecaller model
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
other (please describe below)
Other demo data information
No response