BCFTools
This is a singularity image to deploy bcftools.
This will produce a Singularity image (suitable for running in a cluster environment) using https://hub.docker.com/r/broadinstitute/picard/. We do this by way of a bootstrap file for the Docker image.
1. Install Singularity
Instructions can be found on the singularity site.
2. Bootstrap the image
sudo singularity create --size 4000 bcftools.img
sudo singularity bootstrap bcftools.img Singularity
3. Run commands
How to access the bcftools runtime executable?
./bcftools.img
Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
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
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.