Brent Pedersen

Hi, I agree it would be nice to have that option to only output bases in the --by, but I don't intend to implement since that's easily had by later...

Hi Jessica. I'm looking into this now. I have started a branch here to explore: https://github.com/brentp/slivar/tree/csq I should have progress in the next 3 weeks to know at least if...

Hi, can you try out this file: https://raw.githubusercontent.com/brentp/slivar/83591adf2d154c45ecf5e64c87e4ba1635e874b6/js/csq.js ? then you can do commands like: ``` ./slivar expr \ --js js/csq.js \ -v tests/test.vcf \ --pass-only \ --info "CSQs(INFO.CSQ, VCF.CSQ,...

> Can you provide an example of how we would, e.g. filter for variants that both pass INFO.genic AND have a SIFT

I documented this in more detail here: https://github.com/brentp/slivar/wiki/CSQ

Hi, for this one: ``` --info "(INFO.highest_impact_order < ImpactOrder.5_prime_UTR) && variant.FILTER == 'PASS'" ``` This is because `ImpactOrder` is a javascript object and a property can't start with a number....

instead of `ImpactOrder.['synonymous']`, you want `ImpactOrder['synonymous']`

I was thinking that we could calculate R2 from the observed genotypes, given a large enough cohort. Then choose, for example the single variant from a block with highest allele...

I don't have a lot of experience in this area, but I guess I'm thinking of something like this: https://www.prsice.info/step_by_step/#clumping

did you run ldconfig after installing htslib? and make sure that directory is inclduded on your ld.so.conf?