{"repo":"nf-core/phaseimpute","free":true,"listed":false,"github":"https://github.com/nf-core/phaseimpute","clone":"git clone https://github.com/nf-core/phaseimpute.git","description":"A bioinformatics pipeline to phase and impute genetic data","language":"Nextflow","stars":32,"topics":["genomics","genotype","imputation","low-pass-sequencing","phasing","pipeline","nextflow","workflow","bioinformatics","nf-core"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/phaseimpute is a bioinformatics pipeline to phase and impute genetic data. The whole pipeline consists of five main steps, each of which can be run separately and independently. Users are not required to run all steps sequentially and can select specific steps based on their needs: 1. QC: Chromosome Name Check : Ensures compatibility by validating that all expected contigs are present in the variant and alignment files. 2. Simulation ( --simulate ) : Generates artificial datasets by downsampling high-density data to simulate low-pass genetic information. This enables the comparison of imputation results against a high-quality dataset (truth set). Simulations may include: - Low-pass data generation by downsampling BAM or CRAM files with samtools view -s at different depths. 3. Panel Preparation ( --panelprep ) : Prepares the reference panel through phasing, quality control, variant filtering, and annotation. Key processes include: - Normalization of the reference panel to retain essential variants. - Phasing of haplotypes in the reference panel using Shapeit5. - Chunking of the reference panel into specific regions across chromosomes. - Position Extraction for targeted imputation sites. 4. Imputation ( --impute ) : This is the primary step, where genotypes in the target dataset are imputed using the prepared reference panel. The main steps are: - Imputation of the target dataset using tools like Glimpse1, Glimpse2, Stitch, Quilt, Beagle5 or Minimac4. - Lig","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/phaseimpute/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}