No SV result for non-human samples

[hyunjokoo]

Ask away!

Hello,

When I used DEMO data provided in this github, I got both SV and SNP results. But, when I tried my plant data for wf-human-variation, I got only SNP result. For SV, it said "The workflow found no structural variants to report.".

The followings are my commands. nextflow run epi2me-labs/wf-human-variation -w epi2me-human-variation3/workspace -profile standard -with-docker --bam sangdong-namua_minimap2_to_its_assembly_sorted.bam --ref nd.asm.fasta --sample_name sangdong-namu --snp --sv --out_dir epi2me-human-variation3 --threads 79 --annotation false --bed nd.asm.bed

nextflow run epi2me-labs/wf-human-variation -w epi2me-human-variation1/workspace -profile standard -with-docker --bam m64238e_230920_070508.hifi_reads.bc2032--bc2032_dorado-aligner-to-bc2031_sorted.bam --ref assembly/bc2031_nd-hh-q5.asm.fasta_nextpol-long2.fasta --sample_name bc2032_to_bc2031 --snp --sv --out_dir epi2me-human-variation1 --threads 79 --annotation false --bed assembly/bc2031_nd-hh-q5.asm.fasta_nextpol-long2.bed

For the bottom command, when I used Sniffles2 alone, I got lots of SV results.

Could you please tell me how I can make Sniffles work in wf-human-variation with non-human samples?

Thank you. HJK

[RenzoTale88]

@hyunjokoo it could be related to the filtering applied by the workflow after calling the SVs. You can find the original SVs computed by Sniffles in one of the working directory, I'm happy to point you to the right one if you're happy to share the log file.

[hyunjokoo]

Hello,

Could you please tell me which one is the log file?

I have these files/folders in the result folder.

bc2031_nd-hh-q5.asm.fasta_nextpol-long2.fasta bc2031_nd-hh-q5.asm.fasta_nextpol-long2.fasta.fai bc2032_to_bc2031.mosdepth.global.dist.txt bc2032_to_bc2031.mosdepth.summary.txt bc2032_to_bc2031.readstats.tsv.gz bc2032_to_bc2031.regions.filt.bed.gz bc2032_to_bc2031.thresholds.bed.gz bc2032_to_bc2031.wf-human-alignment-report.html bc2032_to_bc2031.wf-human-snp-report.html bc2032_to_bc2031.wf-human-sv-report.html bc2032_to_bc2031.wf_snp.vcf.gz bc2032_to_bc2031.wf_snp.vcf.gz.tbi bc2032_to_bc2031.wf_sv.vcf.gz bc2032_to_bc2031.wf_sv.vcf.gz.tbi empty_clinvar.vcf execution input.1 jbrowse.json OPTIONAL_FILE ref_cache workspace

Do you mean the processing list during workflow running? I think the attached file is most similar to that one. report.zip

Thank you. HJK

[RenzoTale88]

Apologies, I was not very clear. Could you please share the .nextflow.log file, or alternatively the execution/trace.txt in your output folder?

[hyunjokoo]

Hello,

I do not have nextflow.log file. I attach the trace file.

trace.zip

Thank you. HJK

[RenzoTale88]

You can find the pre-filter sniffles output file in the path: workspace/d5/b9489c*/bc2032_to_bc2031.sniffles.vcf

[hyunjokoo]

Thank you for locating the Sniffles2 result file. I am curious why the Sniffles2 result is not shown in the sv result html file. Could you please tell me how I can put sv result in sv result html file?

Also I tried this option, --sniffles_args '--minsupport 5 --mosaic' but it failed. I found that --mosaic made the workflow failed. When I tried only this option, --sniffles_args '--minsupport 5', it worked. Could you please tell me the guide to add sniffles option?

Thank you. HJK

[RenzoTale88]

You can try lowering the --min_read_support and --min_read_support_limit to make the coverage requirement for a SV less stringent, or set it to 0 altogether, and see if that works.

The workflow uses Sniffles2 v2.0.7, therefore you need to use --sniffles_args '--minsupport 5 --non-germline'.