CalliNGS-NF

Variant caller

A Nextflow pipeline for RNA sequencing variant calling with GATK best practices

GATK RNA-Seq Variant Calling in Nextflow

GitHub

132 stars
9 watching
55 forks
Language: Nextflow
last commit: almost 2 years ago
Linked from 1 awesome list

bioinformaticsgatkgenomicsnextflowngsrna-seqvariant-calling

Backlinks from these awesome lists:

Related projects:

Repository Description Stars
nf-core/sarek Automated workflow for detecting germline or somatic variants in genomic sequencing data 409
nextflow-io/crg-course-nov16 A tutorial project on using Nextflow and Docker for implementing a RNA-Seq pipeline 23
iarcbioinfo/gatk4-genotypegvcfs-nf Joint calling of genotype variants from multiple cohorts using GATK4 best practices 11
ncsa/genomicscortextvarnextflow A Nextflow-based pipeline for detecting structural variants in whole-genome reads using the Cortex-Var algorithm. 2
guigolab/grape-nf Automated RNA-seq analysis pipeline using Nextflow and Docker/Singularity containers 37
cbcrg/kallisto-nf A tool suite implementing Kallisto and Sleuth RNA-seq analysis pipelines in Nextflow 22
cbcrg/grape-nf A pipeline for RNA-Seq analyses using nextflow 2
nbisweden/wgs-structvar A Nextflow pipeline for running structural variation callers on whole genome sequencing data 15
guigolab/chip-nf Automated pipeline for processing ChIP-seq data 17
iarcbioinfo/mutect-nf A Nextflow-based pipeline for somatic variant calling using mutect 9
iarcbioinfo/needlestack An ultra-sensitive multi-sample variant caller for NGS data 49
brwnj/smoove-nf An automation workflow for detecting structural variations in genomic data using the smoove toolset 12
nextflow-io/rnaseq-nf A pipeline for quantifying genomic features from short read data using Nextflow and various software components. 72
iarcbioinfo/gatk4-haplotypecaller-nf Automates the process of haplotype calling from genotyped BAM files using GATK4 8
qbic-pipelines/icgc-featurecounts Automated pipeline for featureCounts on RNAseq BAM files from ICGC datasets 3