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: 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
|