GVCF_pipeline-nf
GVCF generator
Generates GVCF from BAM files using GenomeAnalysisTK with realignment and recalibration steps
Nextflow pipeline for generate GVCF from BAM with GenomeAnalysisTK with step of realignment
4 stars
10 watching
4 forks
last commit: about 8 years ago
Linked from 1 awesome list
Related projects:
Repository | Description | Stars |
---|---|---|
iarcbioinfo/gatk4-haplotypecaller-nf | Automates the process of haplotype calling from genotyped BAM files using GATK4 | 8 |
iarcbioinfo/gatk4-genotypegvcfs-nf | Joint calling of genotype variants from multiple cohorts using GATK4 best practices | 11 |
iarcbioinfo/iarc-nf | Provides a collection of pre-configured bioinformatics pipelines and tools for analyzing next-generation sequencing data. | 47 |
iarcbioinfo/bam_realignment-nf | An automated BAM realignment pipeline using samtools, bwa and sambamba. | 1 |
cbcrg/grape-nf | A pipeline for RNA-Seq analyses using nextflow | 2 |
andremrsantos/next-pipes-lghm | A collection of Nextflow pipelines for analyzing NGS data from the LGHM bioinformatics lab | 3 |
nbisweden/wgs-structvar | A Nextflow pipeline for running structural variation callers on whole genome sequencing data | 15 |
iarcbioinfo/mutect-nf | A Nextflow-based pipeline for somatic variant calling using mutect | 9 |
iarcbioinfo/mpileup-nf | Computation pipeline for calculating genomic coverage from sequencing data using samtools mpileup | 1 |
guigolab/grape-nf | Automated RNA-seq analysis pipeline using Nextflow and Docker/Singularity containers | 37 |
crg-cnag/callings-nf | A Nextflow pipeline for RNA sequencing variant calling with GATK best practices | 132 |
qbic-pipelines/icgc-featurecounts | Automated pipeline for featureCounts on RNAseq BAM files from ICGC datasets | 3 |
nf-core/rnafusion | A bioinformatics pipeline for detecting and analyzing gene fusions from RNA sequencing data | 144 |
iarcbioinfo/bametrics-nf | Tools for computing average metrics from reads overlapping given positions | 1 |
cdcgov/mycosnp-nf | An analysis pipeline for whole genome sequencing of fungal organisms. | 37 |