PMDtools

Tools and workflows for accessing, querying, and analyzing data from the 1000 Genomes Project (1KGP) — the largest public catalog of human genetic variation with whole-genome sequences from 3,202 indi

2 shared topics • 1 shared operation

distiller-nf — Nextflow pipeline for reproducible Hi-C data processing. Aligns Hi-C FASTQ reads with BWA, parses alignments into pairs with pairtools, filters PCR duplicates, and aggregates contacts i

2 shared topics • 1 shared operation

GATK VQSR (Variant Quality Score Recalibration) — machine learning-based variant filtering for GATK Best Practices germline pipelines. Trains a Gaussian mixture model on truth/training resource datase

2 shared topics • 1 shared operation

Tools for manipulating next-generation sequencing data stored in SAM/BAM/CRAM format, including sorting, indexing, and format conversion.

2 shared topics • 1 shared operation

SnpSift -- Java-based toolset for filtering, annotating, and manipulating annotated VCF files from SnpEff or other variant callers. Provides expression-based filtering (filter), database annotation wi

2 shared topics • 1 shared operation