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Releases: brentp/slivar

tsv fix

22 Dec 21:10
@brentp brentp
v0.2.1
ceb97b2
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tsv fix

v0.2.1

  • add INFO.highest_impact_order so user can do things like:

    --info "INFO.highest_impact_order == ImpactOrder.missense"

    to get only missense mutations. or

    --info "INFO.highest_impact_order <= ImpactOrder.missense"

    to get variants with an impact of missense or higher. (note that lower values have higher impact)

  • tsv: bugfix!! previously, slivar tsv used a < 0 check where it should hvae used <= 0 so
    candidates with a parental sample at index 0 in the samples of the vcf would have missing information
    for depth, GQ, and AB. (#78 . Thanks @amwenger for finding the problem and its source).

  • expr: always annotate variant and INFO even if no sample (or trio,group,fam) expressions are given so one can use slivar just to get the 'impactful' annotation.

  • remove duplicates from default-order.txt

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing. (but you'll likely want the javascript included in this repo and the gnotation files linked below)
users can also use slivar via docker at brentp/slivar:v0.2.1
The pslivar binary allows running slivar expr commands in parallel

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 4
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minor bugfix

05 Nov 17:28
@brentp brentp
v0.2.0
40ee56d
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minor bugfix

v0.2.0

  • clear values from expressions for family, group, and sample. was previously only done for
    trios. so if you relied on something like: 
    --group-expr "expr1: ..." \
--group-expr "expr2:('expr1' in INFO) && ..."\
    then the expr2 would still see expr1 in INFO even if the preceding expression did not pass but it
    has passed for a previous variant. Thanks Amelia Wallace for finding and reporting a simple test-case.
  • add /opt/slivar/slivar-functions.js to docker image (#75)

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing. (but you'll likely want the javascript included in this repo and the gnotation files linked below)
users can also use slivar via docker at brentp/slivar:v0.2.0
The pslivar binary allows running slivar expr commands in parallel

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 4
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bugfix for vcfs with >256 info fields

14 Oct 19:10
@brentp brentp
v0.1.13
8cf3a24
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bugfix for vcfs with >256 info fields

v0.1.13

  • fix bug with VCFs with >256 info fields (#74). Thanks @liserjrqlxue for making a great test-case.

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing. (but you'll likely want the javascript included in this repo and the gnotation files linked below)
users can also use slivar via docker at brentp/slivar:v0.1.13

The pslivar binary allows running slivar expr commands in parallel

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 4
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features, bugfixes, compound-het fixes

21 Aug 16:21
@brentp brentp
v0.1.12
97859c0
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features, bugfixes, compound-het fixes

This adds small improvements except for large bug-fix for compound-hets for families with multiple affected kids. Previously, a shared compound-het would only be reported for one of the kids. This now fixed. See below for full changelog.

v0.1.12

  • slivar expr: handle ploidy > 2 (updated hts-nim) (#55 thanks to @markw3lsh for reporting and providing a test-case)
  • slivar: optionally support strings in format (sample) fields. default is to ignore these for performance reasons, but users can set the environment variable SLIVAR_FORMAT_STRINGS to anything to force slivar to populate the javascript objects with any strings in the VCF. e.g. SLIVAR_FORMAT_STRINGS=1 slivar expr ... and use unset SLIVAR_FORMAT_STRINGS to remove. (#37)
  • slivar compound-hets: fix bug with 2 affect sibs sharing same compound-het previously only 1 sib would be reported

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing. (but you'll likely want the javascript included in this repo and the gnotation files linked below)
users can also use slivar via docker at brentp/slivar:v0.1.12

The pslivar binary allows running slivar expr commands in parallel

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 4
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parallel slivar and INFO.genic

03 Mar 22:32
@brentp brentp
v0.1.11
5d6a599
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parallel slivar and INFO.genic

This release is the first where pslivar (parallel slivar) is well tested. It handles running slivar expr in parallel (by genomic region) see wiki page for more detail.

This also adds INFO.genic for VCFs that have been annotated with VEP, snpEff, or bcftools. This complements INFO.impactful, but mainly adds synonymous variants to consideration. See the wiki for more detail.

Full changes below:
v0.1.11

  • gnotate: ~10-20% speed improvement by inlining cmp in binarysearch
  • slivar expr: fix counts in summary table when some families in the cohort have no affected samples
  • slivar tsv: improve readability when 1 or both parents are missing
  • slivar tsv: fix comma separation with 1 or both parents missing (thanks @brwnj for reporting)
  • slivar ddc: when looking at all chromosomes, skip X, Y
  • slivar expr: add --exclude option which takes a bed file of exclude regions
  • slivar compound-hets: default will now output compound-het pairs that include synonymous variants
  • pslivar: fix tsv output from pslivar (which allows running slivar in parallel). more info here
  • add INFO.genic boolean to complement INFO.impactful. By default this includes all impacts included by impactful along with
    synonymous and other exonic, but non-protein-altering variants (but does not include intronic. (more info here

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing. (but you'll likely want the javascript included in this repo and the gnotation files linked below)
users can also use slivar via docker at brentp/slivar:v0.1.11

The pslivar binary allows running slivar expr commands in parallel

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 4
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fixes for data-driven cutoffs.

14 Jan 17:33
@brentp brentp
v0.1.10
917aa1a
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fixes for data-driven cutoffs.

v0.1.10

  • [slivar ddc] fix bug when selecting sample filters.
  • [slivar ddc] UI fix: remove button when [x] is clicked.

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.10

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 3
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data-driven-cutoffs and family expressions for rare disease

10 Jan 17:46
@brentp brentp
v0.1.9
ccfd8bb
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data-driven-cutoffs and family expressions for rare disease

v0.1.9

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.9

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 3
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bug-fix for subsetting vcfs

20 Nov 21:53
@brentp brentp
v0.1.8
6ac9be1
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bug-fix for subsetting vcfs

v0.1.8

  • fix bug when subsetting vcfs (ped file contained subset of samples in vcf). Thanks Matt for reporting.

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.8

gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

Assets 3
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bug-fixes and gnomad genomes v3

05 Nov 16:32
@brentp brentp
v0.1.7
e1e4955
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bug-fixes and gnomad genomes v3

this release has small bugfixes and general usability experiments. see below for the list of changes and the links to the gnotate (zip) file for hg38 genomes from gnomad.

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.7

Full release notes:

v0.1.7

  • slivar make-gnotate will error with warning if field is not a float or int
  • compound-het provides a way to ignore some impacts (intron, non_coding, etc) and sets sane defaults. this removes
    most candidates from WGS which were predominantly pairs of intronic or non-coding variants.
  • compound-het: remove -f flag, this is now discovered by default
  • only samples with parents in the vcf (not just ped) are counted as trios
  • expose sample.phenotype attribute which is a string taken directly from the pedigree file
  • given an error on an INFO expression, don't bail, just report and continue
  • fix for VCFs without index AND without contigs in header (#44)
  • support for file sizes > 4.2GB and support for gnotate files with chr prefix annotating query files without
  • fix gnotate bug where some long alleles were not annotated
gnotate annotation files

the gnotation files for fast annotation remain unchanged except for the addition of topmed.
Users can create their own gnotation files with slivar make-gnotate, but we provide:

  • gnomad for hg37 with AF popmax, numhomalts (total and controls only) here
  • gnomad for hg38 with AF popmax, numhomalts (updated in release v0.1.2) here

+ gnomad genomes (71,702 samples) for hg38 with AF popmax, numhomalts (updated in release v0.1.7) here
This zip file is broken. Will be updated soon.

Assets 3
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family-based filtering and `impactful`

31 Jul 18:44
@brentp brentp
v0.1.6
a135a87
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family-based filtering and `impactful`

until this release slivar was heavily focused on trio expressions. but this left quads and more ragged families as possible but more difficult. this release allows things like:

--family-expr 'aff_only:fam.every(function(s) { s.het == s.affected && s.hom_ref == !s.affected && s.GQ > 15 })'

to extract variants where all affecteds in a family are heterozygotes and all unaffecteds are homozygous reference (and all samples have genotype quality > 15).

This release also introduces INFO.impactul, which is extracted from the consequence field added by VEP, bcftools, or snpEff (or all of them if they are all present). This can be used to exclude, for example synonymous or non-coding or other variants as a way to quickly get candidate variants that are more likely functional. See the wiki for more details.

Installation

Just grab the binary
You can download it and use it without any other software. This is the recommended binary.
wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.6

Full release notes:

v0.1.6

  • add INFO.impactful (boolean) if CSQ/BCSQ/ANN is present. this value will be true of any of those annotation are high enough
  • the impactful flag is automaticaly added to the output VCF for any variant passing through slivar and meeting the criteria (https://github.com/brentp/slivar/wiki/impactful)
  • better checks for length of AD field
  • fix for empty groups (#38)
  • add --family-expr for family expressions like:
    fam.every(function(s) { s.het == s.affected && s.hom_ref == !s.affected && s.GQ > 5 })
  • slivar tsv now outputs a sortable column for highest-impact. it makes use of a default
    list of impact orderings from: https://uswest.ensembl.org/info/genome/variation/prediction/predicted_data.html and
    supplemented with any type seen in bcftools or snpEff.
  • bug fix with gnotate (-g) when annotating a file with a empty chromsome followed by a non-empty (e.g. if chr16_random is mixed in with canonical chromosomes)
Assets 3
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