Name: FSDA
Owner: Computational Biology Lab at the University of Toronto
Description: null
Created: 2015-01-15 21:33:35.0
Updated: 2017-05-24 12:23:50.0
Pushed: 2017-12-03 03:06:37.0
Homepage:
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Size: 285
Language: Python
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README
FSDA: Fragment Size Distribution Analysis for non-invasive prenatal CNV prediction
Requirements
- Python 2.6 or newer
- NumPy & SciPy
- samtools
- bcftools
Pre-process
Use the preprocess.sh script in the preprocess directory to create the required files for prediction. Based on the size of the sample and reference, this can take hours.
Usage:
eprocess.sh [sample_dir] [ref_dir] [prep_dir] [ref_genome] [dbsnp_file]
- sample_dir is the directory containing the .bam and the .bai files for the sample cfDNA data
- ref_dir is the directory containing the .bam and the .bai files for the reference cfDNA data
- prep_dir is the directory where the script puts the created files inside
- ref_genome is path to the reference genome fasta file (e.g. hg19.fa)
- dbsnp_file is path to a list of commons snps for the reference genome, such as snp142Common.txt, obtainable from http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp142Common.txt.gz
Prediction
The script predict_region.sh in the directory prediction can be used to predict the copy number of a region.
Usage:
edict_region.sh [sample_dir] [ref_dir] [prep_dir] [chr] [begin] [end] [ks_threshold] [neighbours_threshold] [fraction]
- sample_dir is the the directory containing the .bam and the .bai files for the sample cfDNA data
- ref_dir is the the directory containing the .bam and the .bai files for the reference cfDNA data
- prep_dir is the the directory containing the files created in the pre-process
- chr is the chromosome of the target region
- begin is the beginning position of the target region
- end is the end position of the target region
- ks_threshold is the threshold for control similarity
- neighbours_threshold is the threshold for the required minimum number of neighbours
- fetal_fraction is the fraction of the cfDNA in the sample that is fetal origin
Example:
edict_region.sh ~/sample_dir ~/ref_dir ~/prep_dir chr3 10000000 11000000 0.002 5 0.13
Reference
Arbabi, Aryan, Ladislav Rampá?ek, and Michael Brudno. “Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.” Bioinformatics 32.11 (2016): 1662-1669.
