Alternatives and similar repositories for somalier

Users that are interested in somalier are comparing it to the libraries listed below

• brentp / slivar
  genetic variant expressions, annotation, and filtering for great good.
  ☆263Updated 3 weeks ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated 3 weeks ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆256Updated 2 years ago
• brentp / mosdepth
  fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
  ☆763Updated 3 weeks ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆256Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆211Updated 5 years ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆379Updated last month
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆270Updated 2 months ago
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆339Updated this week
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆225Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆161Updated 2 years ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆314Updated last week
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆347Updated 3 months ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆195Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆333Updated 3 years ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆183Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆478Updated last week
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆191Updated this week
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆253Updated last year
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆247Updated last month
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆138Updated 4 years ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆369Updated last month
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated 2 weeks ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated last week