SoftSearch

This is the new official repository to house SoftSearch, originally published in PLoS One. It is not under active development, but some people may find it useful. To make deployments simple, we provided an installation script (install.pl), but the recommended way is using Docker.

Option 1. Run using DockerHub

docker run --rm -it stevenhart/softsearch perl softsearch/script/SoftSearch.pl [-cqlrmsd] -b <BAM> -f <Genome.fa>
	-q		Minimum mapping quality [20]
	-l		Minimum length of soft-clipped segment [5]
	-r		Minimum depth of soft-clipped reads at position [5]
	-m		Minimum number of discordant read pairs [5]
	-s		Number of sd away from mean to be considered discordant [6]
	-u		Number of unmated pairs [0]
	-d		Max distance between soft-clipped segments and discordant read pairs [Maximum normal insert]
	-o		Output file name [output.vcf]
	-t		Print temp files for debugging [no|yes]
	-c		use only this chrom or chr:pos1-pos2
	-p		use paired-end mode only. In other words, don't try to find soft-clipping events!
	-g		Enable paired-only seach. This will look for discordant read pairs even without soft clips.
	-a		set the minimum distance for a discordant read pair without soft-clipping info [10000]
	-L		Flag to print out even small deletions (low quality)
	-e		disable strict quality filtering of base qualities in soft-clipped reads [no]
	-blacklist	areas of the genome to skip calling.  Requires -genome_file
	-genome_file	tab seperated value of chromosome name and length.  Only used with -blacklist option

Option 2. Create an environment to launch the container using Docker-Machine.

In this case, I'll just use default, but you can use whatever you want.

docker-machine create -d virtualbox default
eval $(docker-machine env default)

Next clone the repo from GitHub

git clone https://github.com/Steven-N-Hart/softsearch.git
cd softsearch

Now build the image

docker build -t test .

Finally, launch the container. Note, that I am including a directory to mount. This directory should include the paths to your genome.fa file and your BAM file

docker run --rm -it test perl softsearch/script/SoftSearch.pl [-cqlrmsd] -b <BAM> -f <Genome.fa>
	-q		Minimum mapping quality [20]
	-l		Minimum length of soft-clipped segment [5]
	-r		Minimum depth of soft-clipped reads at position [5]
	-m		Minimum number of discordant read pairs [5]
	-s		Number of sd away from mean to be considered discordant [6]
	-u		Number of unmated pairs [0]
	-d		Max distance between soft-clipped segments and discordant read pairs [Maximum normal insert]
	-o		Output file name [output.vcf]
	-t		Print temp files for debugging [no|yes]
	-c		use only this chrom or chr:pos1-pos2
	-p		use paired-end mode only. In other words, don't try to find soft-clipping events!
	-g		Enable paired-only seach. This will look for discordant read pairs even without soft clips.
	-a		set the minimum distance for a discordant read pair without soft-clipping info [10000]
	-L		Flag to print out even small deletions (low quality)
	-e		disable strict quality filtering of base qualities in soft-clipped reads [no]
	-blacklist	areas of the genome to skip calling.  Requires -genome_file
	-genome_file	tab seperated value of chromosome name and length.  Only used with -blacklist option

Option 3. Install on bare metal (not garunteed to work)

git clone https://github.com/Steven-N-Hart/softsearch.git
cd softsearch
perl install.pl -p $PWD