Nextflow Modules
Showing module(s) with keyword "gvcf"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bcftools/convert | Process | bcftools convert vcf gvcf | Converts certain output formats to VCF |
| nf-core/gatk4/combinegvcfs | Process | gvcf gatk4 vcf combinegvcfs short variant discovery | Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file |
| nf-core/gatk4/genotypegvcfs | Process | gatk4 genotype gvcf joint genotyping | Perform joint genotyping on one or more samples pre-called with HaplotypeCaller. |
| nf-core/gatk4/reblockgvcf | Process | gatk4 gvcf reblockgvcf | Condenses homRef blocks in a single-sample GVCF |
| nf-core/glnexus | Process | merge gvcf joint-variant-calling | merge gVCF files and perform joint variant calling |
| nf-core/gvcftools/extractvariants | Process | gvcftools extract_variants extractvariants gvcf vcf | Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file. |
| nf-core/parabricks/genotypegvcf | Process | joint-genotyping gvcf vcf genotypegvcf germline | NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs |
| nf-core/parabricks/indexgvcf | Process | vcf gvcf tbi idx index GPU-accelerated | NVIDIA Clara Parabricks GPU-accelerated gvcf indexing tool. |
| nf-core/sentieon/gvcftyper | Process | joint genotyping genotype gvcf | Perform joint genotyping on one or more samples pre-called with Sentieon's Haplotyper. |
| nf-core/somalier/ancestry | Process | relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family | Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs |
| nf-core/somalier/extract | Process | relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family | Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs |
| nf-core/somalier/relate | Process | relatedness QC bam cram vcf gvcf ancestry identity kinship informative sites family | Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs |