diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 49 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 26 |
2 files changed, 75 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 63934fc..2b1d514 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -499,6 +499,55 @@ reads.") collapses them into a non-redundant graph structure.") (license license:expat))) +(define-public vcfbub + (package + (name "vcfbub") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/vcfbub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0sk2ab22z6qa00j1w8a8f5kbb7q2xb10fhd32zy4lh351v3mqmyg")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2) + ("rust-flate2" ,rust-flate2-1) + ("rust-vcf" ,rust-vcf-0.6)))) + (home-page "https://github.com/pangenome/vcfbub") + (synopsis "Popping bubbles in vg deconstruct VCFs") + (description + "The VCF output produced by a command like @command{vg deconstruct -e -a +-H '#' ...} includes information about the nesting of variants. With @code{-a}, +@code{--all-snarls}, we obtain not just the top level bubbles, but all nested +ones. This exposed snarl tree information can be used to filter the VCF to +obtain a set of non-overlapping sites (n.b. \"snarl\" is a generic model of +graph bubbles including tips and loops). +@code{vcfbub} lets us do two common operations on these VCFs: +@enumerate +@item We can filter sites by maximum level in the snarl tree. For instance, +@code{--max-level 0} would keep only sites with @code{LV=0}. In practice, vg's +snarl finder ensures that these are sites rooted on the main linear axis of the +pangenome graph. Those at higher levels occur within larger variants. +@item We can filter sites by maximum allele size, either for the reference +allele or any allele. In this case, @code{--max-ref-length 10000} would keep +only sites where the reference allele is less than 10kb long. Setting +@code{--max-ref-length} or @code{--max-allele-length} additionally ensures that +the output contains the bubbles nested inside of any popped bubble, even if +they are at greater than @code{--max-level}. +@end enumerate +@code{vcfbub} accomplishes a simple task: we keep sites that are the children +of those which we \"pop\" due to their size. These occur around complex large +SVs, such as multi-Mbp inversions and segmental duplications. We often need to +remove these, as they provide little information for many downstream +applications, such as haplotype panels or other imputation references.") + (license license:expat))) + (define-public gafpack (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 (revision "1")) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index a0e31ce..79832bc 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -575,6 +575,32 @@ or any combination.") (description "Yet another format-preserving TOML parser.") (license (list license:expat license:asl2.0)))) +(define-public rust-vcf-0.6 + (package + (name "rust-vcf") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (crate-uri "vcf" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0dc0p00a19rpmhrqcshrn2qg5l716b5s1fy8vpd3p32bw77vpbs0")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Not all files included + #:cargo-inputs + (("rust-nom" ,rust-nom-7) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-thiserror" ,rust-thiserror-1)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap-2) + ("rust-flate2" ,rust-flate2-1)))) + (home-page "https://github.com/informationsea/vcf-rs") + (synopsis "Rust implmentation of VCF parser") + (description "This package provides a rust implmentation of a VCF parser.") + (license license:asl2.0))) + (define-public rust-gsl-sys (package (name "rust-gsl-sys") |