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Search results for python vcf

207 search results found

Starfish ⭐ 17

Intersect multiple VCF files with haplotype awareness

Haplotypo ⭐ 17

This is the Haplotypo repository

Diploid personal genome assembly and comprehensive variant detection based on linked-reads

Color DNA/RNA bases in terminal output

commandline manipulation of genomic variants and NGS reads

Calculates allelic Fold Change (aFC) using standard input files for fastQTL.

Phenopredict21 ⭐ 15

Command line tool to predict phenotype from VCF (gets models from pheno-server-21)

A Data Fusion Method for Multi Source (VCF4.0+) Structural Variation Analysis

Human mitochondrial variants annotation using HmtVar.

Allelecounter ⭐ 15

Counts the number of reads which map to either the reference or alternate allele at each heterozygous SNP.

Vcf_fdw_postgresql ⭐ 14

A PostgreSQL foreign data wrapper for VCF files.

Clinical Filter ⭐ 14

filtering trio-based genetic variants in VCFs for clinical review

Scripts to handle NGS data and other biological data

Use somatic mutations to choose a personalized cancer vaccine (tumor-specific immunogenic peptides)

Snapperdb ⭐ 14

Misc Genomics Tools ⭐ 13

assorted scripts for doing genomics

vSNP -- validate SNPs

ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.

Sfs Scripts ⭐ 13

A collection of tools useful for preparing or manipulating site-frequency spectrum (SFS) files

Seven Bridges Genomics aligner/caller debugging and analysis tools

Varifier ⭐ 13

Variant call verification

Variant call adjudication

Library for indexing VCF files for random access searches by rsID

Variant_alert ⭐ 12

Variant Alert!, a framework to monitor every significant alteration in variant classification and gene-disease association between two versions of ClinVar database.

Horizontal Gene Transfer Detection by Mapping Sequencing Reads

Svhawkeye ⭐ 12

Collection of Python scripts for parsing/analyses of RAD-seq data

Genomatnn ⭐ 12

Predicts adaptive introgression using a CNN trained on genotype matrices.

Samplot Ml ⭐ 12

Code for building and testing variant ranking strategies

Calling deletions using deep convolutional neural

Ucscbeacon ⭐ 10

A GA4GH Draft Beacon implementation

MoBiDiC Priorization Algorithm

Carddav2asterisk ⭐ 10

Tiny Python script that reads all contacts from a CardDAV addressbook and inserts them into Asterisk's CID lookup database

Causaldb Finemapping Pip ⭐ 10

A GWAS fine-mapping pipeline used in CAUSALdb

Variantconvert ⭐ 9

A customizable genetic variants file format converter.

Vcf Annotator ⭐ 9

Add biological annotations to variants in a given VCF file.

Sequence to Medical Phenotypes: A pipeline featuring variant annotation, prioritization, pharmacogenomics, and tools for analyzing genomic trios (mother, father, child).

Pythonngstools ⭐ 9

Scripts for NGS processing

A simple python library to identify the most likely strain from the population

Distributed and cloud computing framework for vg

The TeddyPi pipeline: Transposable Element detection and discovery for Phylogenetic inference

A population genetics module written in Python

Simulate next-generation sequencing reads for tumor samples

Structural variant pipeline

File_conversions ⭐ 9

Scripts to convert between file formats for various analyses

High Perf Bio ⭐ 9

Open-source toolkit that simplifies and speeds up work with bioinformatics data. high-perf-bio allows you easily upload VCF, BED or arbitrary tables to DB and execute popular bioinformatic queries without MongoDB Query Language knowledge.

Smoove Nf ⭐ 9

Nextflow implementation of the smoove workflow and other tools for SV calling and QC

Fastclone_guanlab ⭐ 8

Svxplorer ⭐ 8

Structural Variant Caller

Aquila_stlfr ⭐ 8

Human haplotype-resolved assembly and variant detection for stLFR, hybrid assembly for linked-reads

Structural variant merging tool

Genetics V2d Data ⭐ 8

Variant to disease dataset workflows for Open Targets Genetics

Analysis Driver ⭐ 8

Pipelines for Illumina HiSeqX demultiplexing, sequence QC and variant calling.

Convert VCF (Variant Call Format) into TCGA MAF (Mutation Annotation Format)

Finding cryptic relationships to boost disease gene detection

Tool for the validation of structural genomic rearrangements using long read sequence data

Divine: Prioritizing Genes for Rare Mendelian Disease in Whole Exome Sequencing Data

Simple genotype comparison of VCF files

Lift Over Vcf ⭐ 7

UCSC liftOver (genome build converter) for vcf format

Automated Tool for Global Screening Array analysis

Vcf Explorer ⭐ 7

Database and interface for vcf files.

Split a BAM file by haplotype support

Tools for calling and comparing variants from simulated read sets

Admixfrog ⭐ 7

Snp_calling_scripts ⭐ 7

Collection of scripts for bacterial SNP calling

Novel insertion detection with 10X reads

Galaxy.consensus ⭐ 7

consensus calling tool for cox Galaxy instance.

Script_collection ⭐ 7

Collection of scripts to solve small bioinformatic challenges.

CNV analysis based on the depth of coverage of Illumina data

VPOT - Variant Prioritisation Ordering Tool. VPOT is a Python tool written to allow prioritisation of variants in ANNOVAR annotated VCF files.

Precisionmedicinetoolkit ⭐ 6

Search public databases for given genotypic information

A library to create and handle counts files used with PoMo.

Gdbigtools ⭐ 6

GDBIGtools: A command line tools for GDBIG varaints browser

Broad Fungalgroup ⭐ 6

Broad Fungal Genomics group scripts

Terra Notebook Utils ⭐ 6

Utilities for the Terra notebook environment.

Keypirinha Ppl ⭐ 6

Call and email people easily

Clinotator ⭐ 6

Clinical interpretation of ambiguous ClinVar annotations

Compbio Galaxy Wrappers ⭐ 6

OHSU Galaxy wrappers.

Vcf2msa.py ⭐ 6

Package for writing multiple sequence alignments of pseudo-references from a VCF file with a reference genome

Ngshelper ⭐ 6

NGShelper is a set of tools useful to performance some tasks related to NGS analysis.

Chrom_sweep ⭐ 6

Sweep-line algorithm for genomic features. Detect overlaps on large files w/ minimal memory.

Plot allele frequencies in VCF files

Python tools for proteogenomics analysis toolkit

Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.

Rgapeppipe ⭐ 5

Reference Guided Assembly Pepperell Lab Pipeline

Oncogemini ⭐ 5

Tools for working with Variant Call Format files.

Variant Annotation, Segregation and Exclusion for family or cohort based rare-disease sequencing studies.

Vcf2diyabc.py ⭐ 5

script that convert vcf file into genotype data matrix to input DIYABC program.

Super sensitive mutation validator, uses sam/bam and vcf

Vcfiterator ⭐ 5

Python module for iterating over a VCF file, parsing and generating data structures.

Vcf Annotate Polyphen ⭐ 5

A tool to annotate human VCF files with PolyPhen2 effect measures

Allows one to manipulate a VCF as a MultiIndex Pandas DataFrame

Germline_variant_snakemake ⭐ 5

Snakemake workflow to call germline variant

Indel_correction_pipeline ⭐ 5

new falcon assemblies that have been quivered and Pilon polished still have heterozygote indel errors. This pipeline will correct most of them.

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