This instructions are for debian based linux distributions such as: Ubuntu, Linux mint, Lubuntu...
All standard python packages required are specified in
the requirements.txt and in setup.py files.
Python 3.5 or later to run ngsCAT2.
In Ubuntu, Mint and Debian you can install Python 3 like this:
$ sudo apt-get install python3 python3-pip
- Samtools samtools 1.7 using htslib 1.7.2 Samtools webpage http://www.htslib.org/download/
sudo apt-get install samtools=1.7-1
- Bedops version 2.4.25 or greater Bedops webpage https://bedops.readthedocs.io/en/latest/content/revision-history.html#v2-4-35
For the installation of the tool just only run:
pip3 install git+https://github.com/alegarsan2/ngsCAT2@master
Usage:
****************************************************************************************************************
Task: Assesses capture performance in terms of sensibility, specificity and uniformity of the coverage.
Output: An html report will be created at the path indicated with the --out option.
*****************************************************************************************************************
usage: ngscat2 --bams <filename> --bed <filename> --out <path> --annotation <filename> --reference <filename> --tmp <path> --threads <integer>
Options:
-h, --help show this help message and exit
--bams=BAMS Required. Comma separated list of bam files (2
maximum). E.g.: --bams
/home/user/bam1.sorted.bam,/home/user/bam2.sorted.bam
--bed=BED Required. Full path to the bed file containing the
target regions.
--out=OUTDIR Required. Full path to the directory where results
will be saved.
--reference=REFERENCE
Optional. String indicating the path to a .fasta file
containing the reference chromosomes. Default=None.
--annotation=ANNOTATION
Optional. String indicating the path to a .bed file
containing annotated regions . Default=None.
--coveragethrs=COVERAGETHRESHOLDS
Optional. Comma separated list of real numbers (do not
leave spaces between) indicating coverage thresholds
to be used when calculating percentages of covered
bases (first graph in the report).
Default=1,5,10,20,30.
--tmp=TMP Optional. String indicating the full path to a
temporary directory where temporary files will be
created. Default=/tmp/.
--threads=NTHREADS Optional. Integer indicating the number of concurrent
threads to launch. Default=cpu_count() - 1.
Here an example of input data can he downloaded.
- Hg0097 alignment data BAM http://ngscat.clinbioinfosspa.es/_media/ngscat/download/hg00097.bam
- Region of interest file BED ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/exome_pull_down_targets/20130108.exome.targets.bed
- Reference genome (for --reference option) http://ngscat.clinbioinfosspa.es/_media/ngscat/download/hg19.wochr.tar.gz
- Annotated bed (for --annotation option) https://mega.nz/#!f2oRxI7Z!QUSRErtvwNGs2tfpwRWjiPZQkOEhRQhaWtXhkmXXpEM
#Output example Exome example https://mega.nz/#!eywTGCBL!6HTDl7J9eLY4VhX2aFfe57Cp9mvwLw4JTcDcHr-zu1A