Nextflow Modules
Showing module(s) with keyword "haplotype"
| Module | Keywords | Description |
|---|---|---|
| nf-core/gatk4/haplotypecaller | gatk4 haplotype haplotypecaller | Call germline SNPs and indels via local re-assembly of haplotypes |
| nf-core/gatk4/mutect2 | gatk4 haplotype indels mutect2 snvs somatic | Call somatic SNVs and indels via local assembly of haplotypes. |
| nf-core/happy/happy | 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 | happy benchmark haplotype | Pre.py is a preprocessing tool made to preprocess VCF files for Hap.py |
| nf-core/happy/sompy | 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 | heteroplasmy homoplasmy mitochondrial mitorsaw haplotype | Mitorsaw analyses mitochondrial variants and identifies heteroplasmy and homoplasmy |
| nf-core/sentieon/haplotyper | sentieon haplotypecaller haplotype | Runs Sentieon's haplotyper for germline variant calling. |
| nf-core/shapeit5/ligate | 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 | phasing haplotype shapeit | Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data. |
| nf-core/shapeit5/phaserare | phasing rare variants haplotype shapeit | Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate). Require feature AVX2. |