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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Coverage and Depth calculations #1659

Open jbague opened 1 month ago

jbague commented 1 month ago

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

asp8200 commented 1 month ago

Hi @jbague 👋

Could the coverage reports from mosdepth be what you're looking for?

https://nf-co.re/sarek/3.4.4/docs/output/#mosdepth

You can find examples of those reports here:

https://nf-co.re/sarek/3.4.4/results/sarek/results-5cc30494a6b8e7e53be64d308b582190ca7d2585/test_full_aws/reports/mosdepth/HCC1395N/

They are part of the output generated by the test_full-profile of Sarek.

In any case, I don't suppose this is a bug, but more a question of getting used to the workings of sarek and the output of sarek. I suggest that you join us over in the Slack channel for Sarek.

https://nf-co.re/join