Nextflow Modules
Showing module(s) with keyword "haplotype"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/gatk4/haplotypecaller | Process | gatk4 haplotype haplotypecaller | Call germline SNPs and indels via local re-assembly of haplotypes |
| nf-core/gatk4/mutect2 | Process | gatk4 haplotype indels mutect2 snvs somatic | Call somatic SNVs and indels via local assembly of haplotypes. |
| nf-core/happy/happy | Process | happy benchmark haplotype validation | Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants. |
| nf-core/happy/prepy | Process | happy benchmark haplotype | Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py |
| nf-core/happy/sompy | Process | happy sompy benchmark haplotype validation somatic variants | Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations. |
| nf-core/mitorsaw/haplotype | Process | heteroplasmy homoplasmy mitochondrial mitorsaw haplotype | Mitorsaw analyses mitochondrial variants and identifies heteroplasmy and homoplasmy |
| nf-core/sentieon/haplotyper | Process | sentieon haplotypecaller haplotype | Runs Sentieon's haplotyper for germline variant calling. |
| nf-core/shapeit5/ligate | Process | ligate haplotype shapeit | Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants. |
| nf-core/shapeit5/phasecommon | Process | phasing haplotype shapeit | Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data. |
| nf-core/shapeit5/phaserare | Process | phasing rare variants haplotype shapeit | Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2. |
| nf-core/vcf_phase_shapeit5 | Workflow | VCF phase shapeit5 haplotype | Subworkflow to phase a reference panel VCF file using SHAPEIT5. The panel is first chunked by chromosome by glimpse2/chunk (if no chunks provided), then genotypes are phased with shapeit5/phasecommon and finally the chunks are merged back together by shapeit5/ligate by chromosomes. Meta map of all channels will be used to perform joint operations. "regionout", "regionoutPadded", "regionSize" keys will be added to the meta map to distinguish the different files before ligation and therefore should not be used. |