Releases: brentp/slivar
compound-het optimization, speed improvements, bug-fixes
v0.1.5
- !!MAJOR: fix bug with
hom_altalias foralts == 2. Since v0.1.3,hom_altwould not get set to false for samples, variants after being set once. coding using e.g.kid.alts == 2is not affected by this bug. - update wiki to simplify rare disease analysis.
- tune javascript in my.js and rare-disease expressions so that many analyses will run
better than twice as fast. - [expr] add
--skip-non-variablewhich further improves speed by not evaluating javascript for a trio if all members are hom-ref or unknown (but can the same variant will
still be evlauated for trios with at least 1 sample that has a variant at that site. - [compound-het] major speed increase for large cohorts.
- [compound-het] remove -i/--index option as this is now discovered from the header for the CSQ/BCSQ field.
binaries and docker
slivar_staticis a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.5
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
-
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
compound-hets on non trios and error messages
v0.1.4
- better error messages on bad VCF
- [tsv] add --csq-column to
slivar tsvto allow extracting extra CSQ fields - general usability improvements
- [compound-het]: support singleton (kid only) or duo's (kid and 1 parent) to compound het. this will give many false positives because
the variants can't be phased, but the number can still be quite small given sufficient filtering on population allele frequency.
requires --allow-non-trios argument
binaries and docker
slivar_staticis a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.
users can also use slivar via docker at brentp/slivar:v0.1.4
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
-
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
drop gnotate + add `hom_ref`/`het`/`hom_alt` boolean sample attributes
In previous versions, there was a slivar gnotate sub-command. This has now been enveloped into slivar expr so a user can specifiy, e.g. slivar expr -g gnomad.hg37.zip -i "INFO.gnomad_popmax_af < 0.001" $vcf (and of course slivar expr still supports --sample-expr, --trio, and --group exressions).
v0.1.3
- add new sample attributes
hom_ref,het,hom_alt,unknownwhich are synonyms ofalts == 0,alts == 1,alts == 2,alts == -1respectively. - remove
slivar gnotatesub-command. the same functionality can be had fromslivar exprwith-gand--info.
binaries and annotation files
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.1.3
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:
general bugfixes and new tsv command
this release has a new command that allows a user to create a spreadsheet from a (slivar) filtered VCF.
See the wiki for full details
v0.1.2
- new sub-command
slivar tsvto output a tab-separated value file from a filtered VCF for final processing
this command also allows adding columns based on the gene the variant is in, such as description of gene
function, pLI, etc. - fix bug where slivar expr would segfault if labels were re-used (now quits with error message)
- better help in
slivar make-gnotate - improve and document output format for
duo-delhttps://github.com/brentp/slivar/wiki/finding-deletions-in-parent-child-duos - add a prelude function with hasSample(INFO, key, sample) to see if sample has been added to info field by previous filter.
- allow outputting summary table to file with
SLIVAR_SUMMARY_FILEenvironment variable - fix for make-gnotate with multiple files (still requires first file to contain all chromosomes)
- allow more kinds of pedigree files (#30)
- change format of slivar compound het field: adds an id that uniquely identifies the pair of variants.
binaries and annotation files
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.1.2
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:
find large de novo deletions in parent-child duos.
v0.1.1
- better checks on missing parents/kids
- new sub-command
duo-delthat uses non-transmission in parent-child duos to find de novo structural deletions.
e.g. a cluster of sites where kid is 0/0 and parent is 1/1 would be a candidate.
see: https://github.com/brentp/slivar/wiki/finding-de-novo-deletions-in-parent-child-duos
for rare disease analysis: https://github.com/brentp/slivar/wiki/rare-disease#full-analysis-for-trios-with-unaffected-parents
binaries and annotation files
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.1.1
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:
better error messages and --sample-exprs
v0.1.0
- allow accessing INFO via
variant.INFOas well asINFO - better error message on missing gnotate file
- add --sample-expr to
slivar exprsub-command to allow applying an expression to each sample:
--sample-expr "hi_quality:sample.DP > 10 && sample.GQ > 20" - expose samples in javascript in
$Sobject, e.g.$S["sampleABC"].DP > 10 && $S["sampleXYZ"].DP > 10
binaries and annotation files
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software. This is the recommended binary. You can wget, chmod +x and start analyzing.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.1.0
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:
comphets fixes
this release provides a mechanism to use the previous filters (INFO fields with samples names) to tell comphets which samples pass for which variants.
v0.0.9
- fix bug without --pass-only. slivar always behaved as if --pass-only was used.
- [compound-hets] fix for multi-sample VCFs with
--sample-field
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.0.9
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:
bugfix release
this release is mostly bugfixes for edge-cases.
v0.0.8
- use random file names so concurrent slivar processes don't clobber files.
- more informative error on bad js expression
- fix for empty groups (#20)
- fix bug when later expressions depended on previous ones.
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.0.8
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files with slivar make-gnotate, but we provide:
support for compound heterozygotes
v0.0.7
- [expr] allow --region to be a bed file
- [compound-hets] new command for finding compound-hets including where 1 side is a de novo (see: https://github.com/brentp/slivar/wiki/rare-disease#compound-heterozygotes)
- default to send output to stdout for streaming
- fix bug in some -g gnotate files
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary. you can download it and use it without any other software.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.0.7
the gnotation files for fast annotation remain unchanged.
Users can create their own gnotation files, but we provide:
gnotation
this release is a huge set of changes that brings slivar to what will likely be it's full set of functionality.
there are substantial improvements to the docs, including several wiki pages describing components of slivar in detail.
one key feature of slivar is annotation (called gnotation). this release allows users to create their own gnotation
databases that allow very fast annotation. For example spliceai provides a 2.2GB file of scores for variants in the exome. slivar can reduce this to 536MB and use it to annotate at ~120K variants/second.
The gnomad zip files reduce exome+genome from a total of ~500GB of data to ~2GB.
Users can create their own gnotation files, but we provide:
- gnomad for hg37 with AF popmax, numhomalts (total and controls only here
- gnomad for hg38 with AF popmax, numhomalts (total and controls only here
- spliceai scores (maximum value of the 4 scores in spliceai) here
There are 2 binaries for this release. Both are 64bit linux binaries.
slivar_staticis a completely static binary.slivar_shareddepends on a libhts.so. it has the advantage of allowing access to files on s3 or https if that is needed.
users can also use slivar via docker at brentp/slivar:v0.0.6
Feedback is appreciated.