BCFtools-Teaching: Difference between revisions
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=== Version === | === Version === | ||
1. | 1.8 | ||
=== Author / Distributor === | === Author / Distributor === | ||
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=== Description === | === Description === | ||
" | "Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants" | ||
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/1.8-foss-2018a | ||
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/1.8-foss-2018a | ||
</pre> | </pre> | ||
| Line 43: | Line 43: | ||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml BCFtools/1. | ml BCFtools/1.8-foss-2018a<br> | ||
bcftools <u>[options]</u><br> | bcftools <u>[options]</u><br> | ||
</div> | </div> | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml BCFtools/1. | ml BCFtools/1.8-foss-2018a | ||
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: 1.8 (using htslib 1.8) | ||
Usage: bcftools [--version|--version-only] [--help] <command> <argument> | Usage: bcftools [--version|--version-only] [--help] <command> <argument> | ||
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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 | ||
sort sort VCF/BCF file | |||
view VCF/BCF conversion, view, subset and filter VCF/BCF files | view VCF/BCF conversion, view, subset and filter VCF/BCF files | ||
| Line 89: | Line 90: | ||
consensus create consensus sequence by applying VCF variants | consensus create consensus sequence by applying VCF variants | ||
cnv HMM CNV calling | cnv HMM CNV calling | ||
csq call variation consequences | |||
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 | ||
mpileup multi-way pileup producing genotype likelihoods | |||
polysomy detect number of chromosomal copies | polysomy detect number of chromosomal copies | ||
roh identify runs of autozygosity (HMM) | roh identify runs of autozygosity (HMM) | ||
Latest revision as of 15:44, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
1.8
Author / Distributor
Description
"Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants" More details are at BCFtools
Running Program
The last version of this application is at /usr/local/apps/eb/BCFtools/1.8-foss-2018a
To use this version, please load the module with
ml BCFtools/1.8-foss-2018a
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/1.8-foss-2018a
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/1.8-foss-2018a
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: 1.8 (using htslib 1.8)
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
sort sort VCF/BCF file
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
csq call variation consequences
filter filter VCF/BCF files using fixed thresholds
gtcheck check sample concordance, detect sample swaps and contamination
mpileup multi-way pileup producing genotype likelihoods
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