usage: variant_call.py [-h] -type TYPE -readsdir DIR -outdir OUTPUT_FOLDER
-index INDEX [-steps STEPS] -analysis ANALYSIS_NAME
[-config CONFIG] [-suffix SUFFIX]
[-filenames FILENAMES] [-cluster CLUSTER]
Variant Calling pipeline for Illumina PE/SE data.
Required arguments:
-type Type of reads: SE or PE
-readsdir Path to Sequencing Reads Data directory. Requires full/absolute path.
-outdir Output Folder Path ending with output directory name to save the results. Requires full/absolute path.
-index Reference Index Name. Most Frequently used reference genomes index options: KPNIH1 | MRSA_USA_300 | MRSA_USA_100 | CDIFF_630 | paris
-steps Variant Calling Steps in sequential order.
1. All: This will run all the steps starting from cleaning the reads to variant calling;
2. clean,align,post-align,varcall,filter,stats : This will also run all steps starting from cleaning to variant calling.
3. coverage_depth_stats: Run Only Depth of Coverage Stats module after cleaning and read mapping steps
4. core_prep: Run this step before running the core steps. This will prepare the data required for generating core SNPs
5. core: extract core snps and generate diagnostics plot data matrices to explore filtered snps.
-analysis Unique analysis name that will be used as prefix to saving results and log files.
Optional arguments:
-config Path to Config file, Make sure to check config settings before running pipeline
-suffix Fastq reads suffix such as fastq, fastq.gz, fq.gz, fq; Default: fastq.gz
-filenames fastq filenames with one single-end filename per line. if the type is set to PE, it will detect the second paired-end filename with the suffix from first filename.
-cluster Run variant calling pipeline in one of the four modes. Default: local. The possible modes are: cluster/parallel-cluster/parallel-local/local