https://github.com/lh3/chm-eval
https://github.com/lh3/chm-eval
bioinformatics genomics variant-calling
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/lh3/chm-eval
- Owner: lh3
- License: mit
- Created: 2016-05-11T19:03:16.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2020-06-24T15:25:22.000Z (almost 6 years ago)
- Last Synced: 2025-01-18T14:29:08.729Z (over 1 year ago)
- Topics: bioinformatics, genomics, variant-calling
- Language: TeX
- Size: 524 KB
- Stars: 53
- Watchers: 10
- Forks: 8
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
## Getting Started
```sh
# Download and install evaluation suite (Linux only)
curl -L https://github.com/lh3/CHM-eval/releases/download/v0.4/CHM-evalkit-20180221.tar \
| tar xf -
# Call CHM1-CHM13 variants in the GRCh37 coordinate (will take a while...)
wget -qO- ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR134/ERR1341796/CHM1_CHM13_2.bam \
| freebayes -f hs37.fa - > CHM1_CHM13_2.raw.vcf
# Filter (use your own filters if you like)
CHM-eval.kit/run-flt -o CHM1_CHM13_2.flt CHM1_CHM13_2.raw.vcf
# Distance-based evaluation
CHM-eval.kit/run-eval -g 37 CHM1_CHM13_2.flt.vcf.gz | sh
more CHM1_CHM13_2.flt.summary
# Evaluating allele and genotype accuracy (Java required)
CHM-eval.kit/rtg format -o hs37.sdf hs37.fa # if you haven't done this before
CHM-eval.kit/run-eval -g 37 -s hs37.sdf CHM1_CHM13_2.flt.vcf.gz | sh
more CHM1_CHM13_2.flt.rtg.summary
```
## Introduction
CHM-eval, aka Syndip, is a benchmark dataset for evaluating the accuracy of
small variant callers. It is constructed from the PacBio assembilies of two
independent [CHM][CHM] cell lines using procedures largely orthogonal to the
methodology used for short-read variant calling, which makes it more
comprehensive and less biased in comparison to existing benchmark datasets. The
following figure briefly explains how this dataset was generated:
The truth data can be downloaded from the [release page][release]. The package
contains the list of confident regions, *phased* variant calls including
thousands of long insertions/deletions, and evaluation scripts (see below).
Illumina short reads sequenced from the two cell lines and from the
experimental mixture of the two cell lines are availble via project
[PRJEB13208][ena] at ENA.
```
CHM-eval.kit
|-- 00README.md # this file
|-- 01ori
| |-- func-37d5.bed.gz -> func-37m.bed.gz
| |-- func-37m.bed.gz # coding and conserved regions (from EnsEMBL) in GRCh37
| |-- func-38.bed.gz # coding and conserved regions in GRCh38
| |-- syndip.m37d5.bed.gz # confident regions including poly-A (for alignment against GRCh37+decoy)
| |-- syndip.m37m.bed.gz # for alignment against GRCh37 primary assembly without decoy
| `-- syndip.m38.bed.gz # for alignment against GRCh38 primary assembly
|-- RTG-LICENSE.txt
|-- RTG.jar # rtg-tools v3.8.4 (for evaluating allele/genotype accuracy)
|-- full.37d5.bed.gz # whole-genome confident regions excluding poly-A (against GRCh37+decoy)
|-- full.37d5.vcf.gz # whole-genome phased variant calls, including filtered
|-- full.37m.bed.gz # for alignment against GRCh37 without decoy
|-- full.37m.vcf.gz
|-- full.38.bed.gz # for alignment against GRCh38
|-- full.38.vcf.gz
|-- func.37d5.bed.gz # intersection of full.37d5.bed.gz and 01src/func-37d5.bed.gz
|-- func.37m.bed.gz
|-- func.38.bed.gz
|-- hapdip.js # script for evaluating distance-based accuracy
|-- htsbox # htsbox-r345; auxiliary tool
|-- k8 # k8 javascript shell, for running hapdip.js
|-- rtg # rtg portal script
|-- rtg.cfg
|-- run-eval # key evaluation script
|-- sdust30-37d5.bed.gz # low-complexity regions identified with SDUST at T=30
|-- sdust30-37m.bed.gz -> sdust30-37d5.bed.gz
|-- sdust30-38.bed.gz
|-- um35-hs37d5.bed.gz # universal mask for GRCh37+decoy; for 35bp reads (Mallick et al, 2016)
`-- um75-hs37d5.bed.gz # for 75bp or longer reads
```
If you use this dataset, please cite:
> Li H, Bloom JM, Farjoun Y, Fleharty M, Gauthier L, Neale B, MacArthur D
> (2018) A synthetic-diploid benchmark for accurate variant-calling
> evaluation. *Nat Methods*, **15**:595-597. [PMID:30013044]
[CHM]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729092/
[ena]: https://www.ebi.ac.uk/ena/data/view/PRJEB13208
[release]: https://github.com/lh3/CHM-eval/releases