slivar

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make-gnotate problems

1

`slivar_static make-gnotate *.bgz` Seems to only have processed chr10? ``` > slivar version: 0.1.11 5d6a5990fc06b52cbb1930806d03f786cf27d267 @["make-gnotate", "gnomad.genomes.v3.1.sites.chr10.vcf.bgz", "gnomad.genomes.v3.1.sites.chr11.vcf.bgz", "gnomad.genomes.v3.1.sites.chr12.vcf.bgz", "gnomad.genomes.v3.1.sites.chr13.vcf.bgz", "gnomad.genomes.v3.1.sites.chr14.vcf.bgz", "gnomad.genomes.v3.1.sites.chr15.vcf.bgz", "gnomad.genomes.v3.1.sites.chr16.vcf.bgz", "gnomad.genomes.v3.1.sites.chr17.vcf.bgz", "gnomad.genomes.v3.1.sites.chr18.vcf.bgz", "gnomad.genomes.v3.1.sites.chr19.vcf.bgz", "gnomad.genomes.v3.1.sites.chr1.vcf.bgz", "gnomad.genomes.v3.1.sites.chr20.vcf.bgz", "gnomad.genomes.v3.1.sites.chr21.vcf.bgz", "gnomad.genomes.v3.1.sites.chr22.vcf.bgz",...

mvelinder

group alias description for multiple alleles

8

I'm trying to find differing alleles in a proband with multiple unaffected siblings My alias file looks as follows: ``` #proband sibling s1 s2,s3,s4 ``` with my group expression as...

vdejager

make-gnotate dbSNP change `RS` from `Integer` to `Float`

10

Since dbSNP vcf is huge (15G) from https://ftp.ncbi.nih.gov/snp/latest_release/VCF/ . I want to use slivar to annotate `RS` ``` ##INFO= ``` use origin file `GCF_000001405.25.gz`, I got error message:`input should be...

liserjrqlxue

Provide warning/notification if 0 is in affected_status column of ped

2

To let the user know slivar is treating 0 as unafffected

mvelinder

slivar rare-disease

2

most people will run the rare-disease pipeline as-is. this can be made faster an easier with an interface like: ``` slivar rare-disease \ --min-depth 10 \ --ab 0.2 \ --min-gq...

brentp

multiple SNP in non-coding regions

1

Dear Brent, I'd like to use slivar to look for multiple SNPs co-occurring in a few defined non-coding spaces. I have an aggregate vcf file that has several samples and...

stefanucci-luca

make-gnotate issue when specifying multiple vcf/bcfs

2

Hey there, I'm noticing when using make-gnotate with multiple gnomad vcf.gz files which you described as such: ``` slivar make-gnotate --prefix gnomad-2.1 \ --field controls_nhomalt:gnomad_nhomalt \ --field popmax_AF:gnomad_popmax_af \ gnomad.exomes.r2.1.sites.vcf.bgz...

cvlvxi

Feature Request: Linkage analysis?

1

I'm definitely pushing it too far, but is it possible to implement linkage analysis using Slivar? If you already have alternate tools that you or others have developed, can you...

nroak

ENH: add support for annovar annotations

6

I was trying to use [ANNOVAR](http://annovar.openbioinformatics.org/en/latest/) annotated VCF with the Slivar comphet script. I got the following error: >[noak@nodecn201 cohort_level]$ ~/resources/slivar/slivar compound-hets \ > -v $family.rare.comphet_int2.vcf \ > -f "Gene.refGene"...

nroak

A js function for segregating compound het variants, to be used with `--family-expr`

mvelinder