This is a collection of scripts developed at the Oklahoma Medical Research Foundation to assist in the analysis of so called "Next Generation Sequencing" data. The bulk are for wrapping together a slew of other tools to build a basic sequence to VCF workflow
Most of the scripts are ruby based and there is also some perl. So hopefully you've got those. The ruby scripts are developed under Ruby MRI 1.9.2. Additionally these scripts are like many somewhat specific to our uses at OMRF & our systems installation. In this case a linux based system with Sun Grid Engine, shared NFS, the Environment Modules Project, and then some of the standard sequencing analysis packages:
Additionally for some of the java based tools above, we've got wrapper shell scripts for the commands so not to run it with the full on java -jar .... command
Download it, set the shebang line if needed & add it to your path or put them somewhere in your path. Hey it passes the "works for us test", so installing isn't a high priority for me.
-
analyze_sequence_to_snps.rb
Main wrapper script, takes a config file & runs pipeline to produce VCFs of SNPs & Indels
-
bwa_aln_qsub_tasked.rb
Simple wrapper to run the aln method of bwa via a SGE task array
-
bwa_sampese_qsub_tasked.rb
Another quick wrapper script for a SGE task array, this time to bwa samse or sampe
-
clc_snp_reader.rb
Deprecated script for doing something to CLC output
-
clc_snp_results_to_linkage_ped.rb
Deprecated script again for doing something to CLC based output
-
convert_fastq_to_sam_qsub_tasked.rb
Wrapper for a SGE task array to convert the fastq input to SAM files
-
count_each_individual.rb
Quick wrapper to DepthOfCoverage a set of BAM files
-
fix_sam_rg_qsub_tasked.rb
Wrapper for SGE task array to force/fix the RG tag in the SAM file(s)
-
fix_vcf_generated_ped.rb
Correct the ped files generated by vcftools by using a full correct ped file template
-
gatk_depth_coverage_summation.rb
Combine GATK DepthOfCoverage outputs, ala count_each_individual.rb & then sum that output
-
make_bam_qsub_tasked.rb
Wrapper for SGE task array to make BAM file(s)
-
snip_reader.rb
Deprecated script again having to do something with CLC
-
vqsr_vcf.rb
Performs the GATK Variant Quality Score Recalibration workflow on a VCF
-
xcnv_to_plink_project.rb
Quick script to ready a plink cnv style project from xhmm xcnv output & a pedigree template
Unless otherwise noted, everything is Copyright (c) 2011-2014 Stuart Glenn, Oklahoma Medical Research Foundation. (OMRF). Essentially under the BSD license, see LICENSE file for full details.