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yekaizhou / duet

SNP-Assisted SV Calling and Phasing Using ONT
BSD 3-Clause "New" or "Revised" License
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[Enhancement] Sniffles as extra sv_caller #5

Closed tuannguyen8390 closed 2 years ago

tuannguyen8390 commented 2 years ago

Hi author team,

I believe it is of interest to add more sv_caller into duet

File sv_calling.py, simply inserting:

elif caller == 'sniffles':
        os.system('sniffles --input ' + aln_path + ' --reference ' + ref_path + ' --vcf ' + sv_calling_home + 'variants.vcf ' + '--output-rnames' + ' --snf' + sv_calling_home + 'variants.snf ' +  ' -t ' + str(thread) + ' --minsvlen ' + str(svlen_thres) + ' --minsupport ' + str(supp_thres))

Obviously, you will need sniffles 2.0.6 install, easily done with conda install -c bioconda sniffles=2.0.6. I've made a fork in my local cluster & can make a PR if this is worthwhile considering.

With Sniffles it is possible to merge the snf file across multiple samples & do joint calling for maximum discovery of SVs in a big cohort (similar with Clair3 GVCF options). But as Duet is developed as an start-to-end pipeline, it is perhaps tricky to deploy in such cases.

By the way, cute SV has several recent releases - latest version 2.0.2 so you might want to check that out & update accordingly😃

Best,

Tuan

yekaizhou commented 2 years ago

@tuannguyen8390 Sure, scheduled for next release to include the new versions of Sniffles and cuteSV.

yekaizhou commented 2 years ago

duet has been updated to v0.6 to incorporate sniffles2 and cutesv2 as the base sv callers.

tuannguyen8390 commented 2 years ago

Thanks !