Open
Description
openedon Sep 19, 2024
Description of the bug
Hello,
I hope you're doing well. I’m a bit confused with a question. I ran the pipeline using the GRCh38 reference genome and Mutect2 in paired tumor-normal files. The entire pipeline completed successfully using nf-sarek version 3.4.3.
However, I’m unsure where I can find the folder or file that contains information about the coverage and depth of the sequences.
I apologize if this is a basic question, and I really appreciate your help.
Thank you!
Command used and terminal output
nextflow run /slgpfs/projects/cli20/cli20901/soft/nf-core-sarek_3.4.3/3_4_3/main.nf -profile singularity --input ./ID091.csv --outdir ./results_ID091 --max_cpus 40 --genome GRCh38 --ngscheckmate_bed false --igenomes_base ./references --wes --tools mutect2
Relevant files
No response
System information
Nextflow v.23.04
Hardware HPC
Executor Slurm
Container engine Singularity
Version of nf-core/sarek 3.4.3
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment