slivar

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argument parser doesn't handle `=` in --arg=value

5

Given an invocation of slivar such as `slivar expr --info="INFO.some_integer >= 2" -v slivar-example.vcf`, a syntax error occurs: > duko.nim(71) compile > Error: unhandled exception: SyntaxError: parse error (line 1)...

tedil

query about PED and trio VCF

2

Hi, I have trio VCF for structural variants. The sequence of my samples in the VCF is Father, Mother. Proband. Does this sequence affect slivar results? I have seen slivar...

prasundutta87

CompHet question

4

Hi Brentp, I have another question regarding the CompHet tagging. Basically, what you have done in the script has no problem. But in our lab (we are clinical diagnostic lab),...

lindakjcao

make-gnotate, gnomAD filter field.

9

Can I use slivar make-gnotate to get the gnomAD (v3.1) FILTER field e.g. "##FILTER=

Elliott77

trio and family expr results

6

Hi Brent, I encountered the following issues and would like to ask you for help. I ran `--family-expr` because I considered fam1(unaffected parents and 3 affected kids) as one cohort....

luceamso

Missing de novo variant

2

Hi @brentp, I type possibly de novo variant and then try to confirm it in slivar. There are cases when slivar does not indicate it. Do you know what criteria...

krukanna

Unknown Consequence Types

12

From annotations in VEP 105, I'm seeing a flurry of warning messages warning: unknown impact "splice_polypyrimidine_tract" warning: unknown impact "splice_donor_region" e.g. ```warning: unknown impact "splice_polypyrimidine_tract" from csq "A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PAX6|ENSG00000007372|Transcript|ENST00000640613|protein_coding||9/12|ENST00000640613.1:c.607-12C>T...```

MattWellie

Slivar tsv functionality w/o family structure

4

Hey Brent, Long time gemini user, and setting up slivar for my group. We focus largely on singletons and used gemini filters like num_het, num_hom_alt to capture variants that are...

nbalanda23

Make gnotate from ExAC downloaded from Gnomad

13

Hi Brent, I would like to make annotated file of ExAC downloaded from [here](https://gnomad.broadinstitute.org/downloads) `All chromosomes VCF 4.56 GiB, MD5: f2b57a6f0660a00e7550f62da2654948` The version of slivar is `0.2.7 71af7d12881ae0590c6d2a97ef2b282cc93fe7c6` I have...

Drdreammaerd

Compound het allele segregation in multi-generational pedigree with multiple affecteds

2

Hey Brent, Here's the pedigree I'm working with: ``` #Kindred_ID Sample_ID Paternal_ID Maternal_ID Sex Affection_Status Project K01 UDN019315 0 0 2 1 A1247-211214-VAR-Botto-UFAGSFAA K01 UDN032463 UDN901989 UDN019315 2 2 A1247-211214-VAR-Botto-UFAGSFAA...

mvelinder