BCFtools-Teaching: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 9: | Line 9: | ||
=== Version === | === Version === | ||
1. | 1.3.1 | ||
=== Author / Distributor === | === Author / Distributor === | ||
| Line 16: | Line 16: | ||
=== Description === | === Description === | ||
" | "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF" | ||
More details are at [http://www.htslib.org/ BCFtools] | More details are at [http://www.htslib.org/ BCFtools] | ||
=== Running Program === | === Running Program === | ||
The last version of this application is at /usr/local/apps/eb/BCFtools/1. | The last version of this application is at /usr/local/apps/eb/BCFtools/1.3.1-foss-2016b | ||
To use this version, please load the module with | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml BCFtools/1. | ml BCFtools/1.3.1-foss-2016b | ||
</pre> | </pre> | ||
| Line 43: | Line 43: | ||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml BCFtools/1. | ml BCFtools/1.3.1-foss-2016b<br> | ||
bcftools <u>[options]</u><br> | bcftools <u>[options]</u><br> | ||
</div> | </div> | ||
| Line 59: | Line 59: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml BCFtools/1. | ml BCFtools/1.3.1-foss-2016b | ||
bcftools --help | bcftools --help | ||
Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs) | Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs) | ||
License: GNU GPLv3+, due to use of the GNU Scientific Library | License: GNU GPLv3+, due to use of the GNU Scientific Library | ||
Version: 1. | Version: 1.3.1 (using htslib 1.3.1) | ||
Usage: bcftools [--version|--version-only] [--help] <command> <argument> | Usage: bcftools [--version|--version-only] [--help] <command> <argument> | ||
| Line 83: | Line 83: | ||
query transform VCF/BCF into user-defined formats | query transform VCF/BCF into user-defined formats | ||
reheader modify VCF/BCF header, change sample names | reheader modify VCF/BCF header, change sample names | ||
view VCF/BCF conversion, view, subset and filter VCF/BCF files | view VCF/BCF conversion, view, subset and filter VCF/BCF files | ||
| Line 90: | Line 89: | ||
consensus create consensus sequence by applying VCF variants | consensus create consensus sequence by applying VCF variants | ||
cnv HMM CNV calling | cnv HMM CNV calling | ||
filter filter VCF/BCF files using fixed thresholds | filter filter VCF/BCF files using fixed thresholds | ||
gtcheck check sample concordance, detect sample swaps and contamination | gtcheck check sample concordance, detect sample swaps and contamination | ||
polysomy detect number of chromosomal copies | polysomy detect number of chromosomal copies | ||
roh identify runs of autozygosity (HMM) | roh identify runs of autozygosity (HMM) | ||
Revision as of 14:25, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
1.3.1
Author / Distributor
Description
"BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF" More details are at BCFtools
Running Program
The last version of this application is at /usr/local/apps/eb/BCFtools/1.3.1-foss-2016b
To use this version, please load the module with
ml BCFtools/1.3.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_BCFtools
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=BCFtools.%j.out
#SBATCH --error=BCFtools.%j.err
cd $SLURM_SUBMIT_DIR
ml BCFtools/1.3.1-foss-2016b
bcftools [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml BCFtools/1.3.1-foss-2016b
bcftools --help
Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
License: GNU GPLv3+, due to use of the GNU Scientific Library
Version: 1.3.1 (using htslib 1.3.1)
Usage: bcftools [--version|--version-only] [--help] <command> <argument>
Commands:
-- Indexing
index index VCF/BCF files
-- VCF/BCF manipulation
annotate annotate and edit VCF/BCF files
concat concatenate VCF/BCF files from the same set of samples
convert convert VCF/BCF files to different formats and back
isec intersections of VCF/BCF files
merge merge VCF/BCF files files from non-overlapping sample sets
norm left-align and normalize indels
plugin user-defined plugins
query transform VCF/BCF into user-defined formats
reheader modify VCF/BCF header, change sample names
view VCF/BCF conversion, view, subset and filter VCF/BCF files
-- VCF/BCF analysis
call SNP/indel calling
consensus create consensus sequence by applying VCF variants
cnv HMM CNV calling
filter filter VCF/BCF files using fixed thresholds
gtcheck check sample concordance, detect sample swaps and contamination
polysomy detect number of chromosomal copies
roh identify runs of autozygosity (HMM)
stats produce VCF/BCF stats
Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
automatically even when streaming from a pipe. Indexed VCF and BCF will work
in all situations. Un-indexed VCF and BCF and streams will work in most but
not all situations.
Installation
Source code is obtained from BCFtools
System
64-bit Linux