v0.3.1

v0.3.1

• add CSQ parsing js code: https://github.com/brentp/slivar/wiki/CSQ
• expose sample.GT
• update impact order to include new effects from VEP (#157, #168)

Installation

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:v0.3.1
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

bugfix 0.2.8 regression for annotation

v0.3.0

• bugfix for 0.2.8 regression where SNPs present in gnotate file would be instead annotated as missing #149.
  This happened when annotating a chromosome after a chromosome present in the query set that was not in the gnotate file
  Thanks very much to Steve @seboyden for reporting and providing a test-case.

Installation

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:v0.3.0
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

bugfix for indels (0.2.8 regression)

This release fixes #149 . Thanks very much to Steve @seboyden for reporting and providing a test-case.
This affected large indels. They would be reported as missing from the gnotate file when in fact they were present.

Installation

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:v0.2.9
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

segregating_dominant_x and CSQ fixes

Installation

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:v0.2.8
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

minor

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:v0.2.7
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

v0.2.6

v0.2.6

• allow specifying QUAL and ID to -i argument to slivar tsv (#104 #105)

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:v0.2.6
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

impact order

v0.2.5

• it was previously not possible to adjust the order of impacts with
  SLIVAR_IMPACTFUL_ORDER. This is now fixed. (#97)

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:v0.2.5
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

bugfix

v0.2.4

• fix long-standing bug (#27) that would cause sigsegv in some cases

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:v0.2.4
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

small bugfixes

v0.2.3

• add feature_fusion to impact order list (#92)
• [compound-hets] write summary even if no variants found

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:v0.2.3
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37

v0.2.2

This release is mostly minor or obscure bug-fixes with several usability improvements and fixes in compound-hets..

v0.2.2

• fix bug with '.' in ALT field (caused message about incorrect number of alts in some cases. thanks Batsal for reporting)
• slivar compound-hets: fix bug with parents specified in ped file but absent from VCF (#79)
• slivar compound-hets: add "intergenic_region" to list of impacts that are skipped by default
• add SLIVAR_NO_REPORT_ALL to prevent reporting variants for familys with no affected samples
• fix bug when creating huge zip files with make-gnotate (#86)
• NOTE: change default min depth in slivar-functions.js to 6. (was 0)
• don't hard-code tmp directory to /tmp (use $TMPDIR)
• [compound-hets] dont fail if no usable variants were found, just issue warning.
  this can happen for small chroms or regions when slivar was parallelized.

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:v0.2.2
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:

• 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 v0.1.8) here

• spliceai scores (maximum value of the 4 scores in spliceai) here

• topmed allele frequencies (via dbsnp) these can be used with INFO.topmed_af. Useful when analyzing data in hg38 because some variants in hg38 are not visible in GRCh37