FermiKit: assembly-based variant calling for Illumina resequencing data.

Bioinformatics
Authors
Keywords
Abstract

UNLABELLED: FermiKit is a variant calling pipeline for Illumina whole-genome germline data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions and structural variations. FermiKit takes about one day to assemble 30-fold human whole-genome data on a modern 16-core server with 85 GB RAM at the peak, and calls variants in half an hour to an accuracy comparable to the current practice. FermiKit assembly is a reduced representation of raw data while retaining most of the original information.

AVAILABILITY AND IMPLEMENTATION: https://github.com/lh3/fermikit

CONTACT: hengli@broadinstitute.org.

Year of Publication
2015
Journal
Bioinformatics
Volume
31
Issue
22
Pages
3694-6
Date Published
2015 Nov 15
ISSN
1367-4811
URL
DOI
10.1093/bioinformatics/btv440
PubMed ID
26220959
PubMed Central ID
PMC4757955
Links
Grant list
GM100233 / GM / NIGMS NIH HHS / United States
U54HG003037 / HG / NHGRI NIH HHS / United States