slivar
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brentp
genetic variant expressions, annotation, and filtering for great good.
Is there a way to pull other annotations from the CSQ field other than the built in INFO.impactful? I see that some of the flags need to be integers or...
Hi Brent, I'm working on setting up a slivar pipeline with @jxchong; we have a number of annotation files that are bed formatted rather than vcf/bcf. Do you have a...
This is to track a new tool for more exhaustive support for compound heterozygotes. The current tool supports probably 90% of use-cases. Other uses include: 1. detecting non-standard compound variants...
I am having difficulty getting slivar expressions to show up when using a VCF generated by GATK Mutect2. The command I am using: ``` ./slivar expr --vcf git_sample.txt \ --alias...
Hello, I tried using slivar on a single trio but I got this error which I do not understand [slivar] 3 samples matched in VCF and PED to be evaluated...
Hello! First of all, thank you for sharing this super useful code! I would like to try using your script on an exome-sequenced trio example that you have analyzed in...
Hi Brent, Thanks so much for SLIVAR and all of your wonderful tools! was just wondering if there are any future plans to generate gnotation files for gnomAD v4- I...
Question not bug: Can you select wildcards for subsetting across samples for a genotype? My use case: Single ancestor line, multiple clones derived from it. Alias file: ``` #ancestor clone...
Do anyone here has a rough idea how much memory do I need to analyze a vcf file of around 10GB using slivar expr? I am new to the software,...
Hi Brent, Following up on #158, I was wondering if it might be possible to have some additional diagnostics provided when duktape errors or warnings are thrown. Specifically, in my...