BCFtools-Teaching: Difference between revisions

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=== Version ===
=== Version ===
1.3.1
1.8
   
   
=== 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"
"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/1.3.1-foss-2016b
The last version of this application is at /usr/local/apps/eb/BCFtools/1.8-foss-2018a


To use this version, please loads the module with
To use this version, please load the module with
<pre class="gscript">
<pre class="gscript">
ml BCFtools/1.3.1-foss-2016b
ml BCFtools/1.8-foss-2018a
</pre>  
</pre>  


Here is an example of a shell script, sub.sh, to run on at the batch queue:  
Here is an example of a shell script, sub.sh, to run on the batch queue:  


<div class="gscript2">
<div class="gscript2">
Line 40: Line 40:
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>   
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>   
<nowiki>#</nowiki>SBATCH --output=BCFtools.%j.out<br>
<nowiki>#</nowiki>SBATCH --output=BCFtools.%j.out<br>
<nowiki>#</nowiki>SBATCH --error=BCFtools.%j.err<br>
   
   
cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml BCFtools/1.3.1-foss-2016b<br>     
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/1.3.1-foss-2016b
ml BCFtools/1.8-foss-2018a
bcftools 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: 1.3.1 (using htslib 1.3.1)
Version: 1.8 (using htslib 1.8)


Usage:  bcftools [--version|--version-only] [--help] <command> <argument>
Usage:  bcftools [--version|--version-only] [--help] <command> <argument>
Line 82: 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
    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 88: 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 14:44, 15 August 2018

Category

Bioinformatics

Program On

Teaching

Version

1.8

Author / Distributor

BCFtools

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.

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Installation

Source code is obtained from BCFtools

System

64-bit Linux

Retrieved from "https://wiki.gacrc.uga.edu/index.php?title=BCFtools-Teaching&oldid=13766"