CHANGES.md

v0.1.12 (dev)

• slivar expr: handle ploidy > 2 (updated hts-nim) (#55 thanks to @markw3lsh for reporting and providing a test-case)

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

v0.1.10

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

v0.1.9

• new command slivar ddc: https://github.com/brentp/slivar/wiki/data-driven-cutoffs
• fix for slivar compound-hets reporting orphaned variants in some cases (thanks Steve Boyden for reporting)
• update to htslib >= 1.10
• change recommended setup for rare disease to use family-based approach, rather than trios as it is more flexible and now well-tested. (https://github.com/brentp/slivar/wiki/rare-disease#full-analysis-for-trios-with-unaffected-parents)
• add VCF object available in javascript which gets populated with VCF.CSQ == ["CONSEQUENCE", "CODONS","AMINO_ACIDS", "GENE", ...] and VCF.ANN, VCF.BCSQ if any or all of those annotations are available in the VCF (see #3)

v0.1.8

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

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

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)

v0.1.5

• !!MAJOR: fix bug with hom_alt alias for alts == 2. Since v0.1.3, hom_alt would not get set to false for samples, variants after being set once.
• 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-variable which 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.

v0.1.4

• better error messages on bad VCF
• [tsv] add --csq-column to slivar tsv to 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

v0.1.3

• add new sample attributes hom_ref, het, hom_alt, unknown which are synonyms of alts == 0, alts == 1, alts == 2, alts == -1 respectively.
• remove slivar gnotate sub-command. the same functionality can be had from slivar expr with -g and --info.

v0.1.2

• new sub-command slivar tsv to 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-del https://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_FILE environment 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.

v0.1.1

• better checks on missing parents/kids
• new sub-command duo-del that 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

v0.1.0

• allow accessing INFO via variant.INFO as well as INFO
• better error message on missing gnotate file
• add --sample-expr to slivar expr sub-command to allow applying an expression to each sample: `--sample-expr "hi_quality:sample.DP > 10 && sample.GQ > 20"
• expose samples in javascript in $S object, e.g. $S["sampleABC"].DP > 10 && $S["sampleXYZ"].DP > 10
• better checking of matching between ped and vcf => don't fail on missing kids

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

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.

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