BCFtools-Teaching
Category
Bioinformatics
Program On
Teaching
Version
1.6
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/1.6-foss-2016b
To use this version, please load the module with
ml BCFtools/1.6-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
cd $SLURM_SUBMIT_DIR
ml BCFtools/1.6-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/1.6-foss-2016b bcftools bcftools --help Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs) Version: 1.6 (using htslib 1.6) 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 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