alimanfoo / vcfnp
Load numpy arrays and HDF5 files from VCF (variant call format)
☆31Updated 7 years ago
Alternatives and similar repositories for vcfnp:
Users that are interested in vcfnp are comparing it to the libraries listed below
- normalize, left-align, trim, validate and clean VCF files☆20Updated 9 years ago
- Stupid Simple Structural Variant View☆25Updated 8 years ago
- pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)☆49Updated 7 years ago
- a wee tool for random access into BGZF files.☆84Updated 6 years ago
- Wrapper for RTG's vcfeval; DEPRECATED!☆21Updated 8 years ago
- a pileup library that embraces the huge☆42Updated 4 years ago
- Reference-free variant discovery in large eukaryotic genomes☆41Updated 3 years ago
- Genome-wide reconstruction of complex structural variants☆39Updated 2 years ago
- program for haplotype phasing from sequence reads and related tools☆25Updated 6 years ago
- create a gemini-compatible database from a VCF☆56Updated 4 years ago
- The integrated pipeline for Indel detection☆17Updated 6 years ago
- ☆37Updated 4 years ago
- Parallel merging, squaring off and ensemble calling for genomic variants☆20Updated 5 years ago
- Samwell: a python package for using genomic files... well☆20Updated 2 years ago
- probability of mendelian error in trios.☆11Updated 9 years ago
- SV detection from paired end reads mapping☆38Updated 14 years ago
- Fast calculations of linkage-disequilibrium in large-scale human cohorts☆42Updated 5 years ago
- Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model☆27Updated last year
- prioritize effects of variant annotations from VEP, SnpEff, et al.☆33Updated 2 months ago
- Graphical assessment of structrial variants using 10x genomics data☆10Updated 7 years ago
- find large indels (in the blind spot between GATK/freebayes and SV callers)☆39Updated 7 years ago
- What's The Function of these genes?☆22Updated 7 years ago
- variant discovery and annotation using GATK and Ensembl☆17Updated 11 years ago
- Analysis toolkit and programming library for k-mer profiles☆30Updated 3 years ago
- Toil workflows for common genomic pipelines☆33Updated 5 years ago
- filtering trio-based genetic variants in VCFs for clinical review☆21Updated 4 years ago
- Approach to identify simple and complex structural genomic rearrangements using a randomized approach☆21Updated 6 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆34Updated last year
- Work for the tree sequence inference paper.☆23Updated 4 years ago
- Consensus assembly and variant calling workflow.☆12Updated 9 years ago