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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Finding de novo/autosomal recessive structural variants using slivar #132

Closed prasundutta87 closed 2 years ago

prasundutta87 commented 2 years ago

Hi

I am attempting to use slivar for finding de novo/autosomal recessive SVs for rare disease. I have a trio VCF file that I generated using sniffles2. I have already pre-filtered my set of variants by my own algorithm/workflow. I was having a look at the javascript file that defines the rules for performing mode of inheritance filtering. Since its a SV VCF file, I don't have some FORMAT field tags such as DP and AD. Do I just need to edit the javascript file and that will be it? I will replace some of the tags there and use it instead to filter SVs using the slivar program.

Regards, Prasun

brentp commented 2 years ago

Yes, you can edit the javascript file and otherwise follow the example here: https://github.com/brentp/slivar/wiki/rare-disease

For snps/indels, Allele balance (AB) is very helpful for filtering, but will likely not work the same way for SVs, so you can use your own fields and remove those checks.

prasundutta87 commented 2 years ago

Hi @brentp ..Thanks a lot for this!