Load numpy arrays and HDF5 files from VCF (variant call format)
☆31Jun 27, 2017Updated 8 years ago
Alternatives and similar repositories for vcfnp
Users that are interested in vcfnp are comparing it to the libraries listed below
Sorting:
- These scripts reformat a VCF into a SQLite database, with R☆15Jul 15, 2021Updated 4 years ago
- A Python package for exploring and analysing genetic variation data☆315Feb 1, 2026Updated last month
- FUSE filesystem for the DNAnexus storage system☆13Jan 26, 2026Updated last month
- A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file☆20Oct 26, 2020Updated 5 years ago
- Parallel merging, squaring off and ensemble calling for genomic variants☆20Sep 17, 2019Updated 6 years ago
- use the noise☆15Apr 15, 2020Updated 5 years ago
- The integrated pipeline for Indel detection☆17Apr 29, 2018Updated 7 years ago
- A phase-aware pharmacogenomic diplotyper for PacBio datasets☆20Dec 9, 2025Updated 2 months ago
- LAAVA: Long-read AAV Analysis☆13Dec 9, 2025Updated 2 months ago
- Genevieve client: using GenNotes, report ClinVar for individual genomes & add consensus notes☆10Aug 2, 2016Updated 9 years ago
- liftover for python, made fast with cython☆97Oct 14, 2025Updated 4 months ago
- Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding☆13Jan 8, 2021Updated 5 years ago
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 8 years ago
- Rails application for storing and parsing clinical exome VCF files. Gene annotations can be retrieved via Biomart integration from Ensemb…☆10May 7, 2017Updated 8 years ago
- Process Illumina instrument data into SAM/BAM/CRAM files.☆10Jan 5, 2026Updated last month
- Lab notebook for people who like the command line.☆11Jun 19, 2024Updated last year
- ☆29Jul 10, 2019Updated 6 years ago
- A small C and Python library for reading PLINK genotype files.☆51Nov 27, 2024Updated last year
- Efficient program for calculating Extended Haplotype Homozygosity (EHH) and Integrated Haplotype Score (iHS)☆45Oct 24, 2019Updated 6 years ago
- A standalone and free application to explore genetics variations from VCF file☆108Apr 27, 2024Updated last year
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 11 months ago
- TIDDIT - structural variant calling☆78Dec 8, 2025Updated 2 months ago
- Utilities to detect and profile `het-kmers`☆12Aug 5, 2024Updated last year
- ☆12Feb 19, 2017Updated 9 years ago
- TRGT Repeat expansion summary☆11Apr 10, 2023Updated 2 years ago
- ☆11Feb 14, 2023Updated 3 years ago
- Sample an approximate number of reads from a fastq file without reading the entire file☆11Jun 20, 2017Updated 8 years ago
- A small, auxiliary index to massively improve parallel fastq parsing☆31Feb 12, 2026Updated 2 weeks ago
- Tool to easily start up an IPython cluster on different schedulers.☆146May 1, 2020Updated 5 years ago
- a cythonized, extended version of the interval search tree in bx☆30Jun 4, 2019Updated 6 years ago
- A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data☆47Dec 6, 2024Updated last year
- Read and write VCF and BCF files☆14Oct 16, 2025Updated 4 months ago
- Cromwell output organizer☆13May 18, 2021Updated 4 years ago
- Efficient storage of same-type, uneven-size arrays☆12Aug 5, 2018Updated 7 years ago
- Sweep-line algorithm for genomic features. Detect overlaps on large files w/ minimal memory.☆10Sep 13, 2011Updated 14 years ago
- edit distance sequence tags and helpers☆12Feb 4, 2021Updated 5 years ago
- A tool kit to manage many variant on desktop computer☆13Jan 13, 2026Updated last month
- Explore and analyze biological sequence data☆17Aug 1, 2024Updated last year
- CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.☆30Feb 20, 2021Updated 5 years ago