Nextflow Modules
Showing module(s) with keyword "plink"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/plink/bcf | Process | plink bcf bed bim fam | Analyses binary variant call format (BCF) files using plink |
| nf-core/plink/bmerge | Process | plink bmerge merge fileset quality control | Merge a second PLINK binary fileset into the first and write a new combined PLINK binary fileset |
| nf-core/plink/exclude | Process | exclude plink variant identifiers | Exclude variant identifiers from plink bfiles |
| nf-core/plink/extract | Process | extract plink subset bfiles | Subset plink bfiles with a text file of variant identifiers |
| nf-core/plink/genome | Process | plink identity-by-descent genetics genome | Calculates identity-by-descent over autosomal SNPs |
| nf-core/plink/indep | Process | plink indep variant pruning bim fam | Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. |
| nf-core/plink/indeppairwise | Process | plink indep pairwise variant pruning bim fam | Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain. |
| nf-core/plink/missing | Process | plink missingness missing genotype rate quality control | Compute sample-based and variant-based missing genotype rates and write a new PLINK binary fileset |
| nf-core/plink/recode | Process | recode bfiles plink whole genome association | Recodes plink bfiles into a new text fileset applying different modifiers |
| nf-core/plink/vcf | Process | plink vcf variant call | Analyses variant calling files using plink |
| nf-core/sequencetools/pileupcaller | Process | genotyping mpileup random draw pseudohaploid pseudodiploid freqsum plink bed eigenstrat | PileupCaller is a tool to create genotype calls from bam files using read-sampling methods |