exoclasma-pipe

Description

exoclasma-pipe is a tool for reads quality control, adapters removing, mapping, and variant calling, a part of upcoming ExoClasma Suite.

Features:

• Pool FastQ quality control via FastQC
• Mapping pipeline: cutadapt + BWA + GATK MarkDuplicates
• Variant calling pipeline: GATK BQSR + GATK HaplotypeCaller

This is a pre-release. Use it at your own risk!

Installation

python3 -m pip install exoclasma-pipe

Command-line dependencies

• SAMtools
• BWA
• BEDtools
• FastQC
• cutadapt
• GATK

First five are available at Ubuntu repos:

apt install samtools samtools bwa bedtools fastqc cutadapt

GATK should be installed into Miniconda environment as described by the developer.

Usage

FastQC

exoclasma-pipe FastQC -f ${file_1} ${mask_1} ${file_2} -d ${output_folder}

Align

exoclasma-pipe Align -u ${unit_json_file}

Unit JSON describes a job for pipeline. It must have the following format:

{
	"ID": "Scc3-WXS",
	"Description": "Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages (SRX11913458)",
	"ParentDir": "testoutput",
	"Input": [
		{
			"Files": {
				"R1": "testdata/test_scc3_R1.fastq.gz",
				"R2": "testdata/test_scc3_R2.fastq.gz",
				"Unpaired": null
			},
			"RG": {
				"Sample": "Scc3",
				"Library": "LY0200-I",
				"Platform": "ILLUMINA",
				"Instrument": "IlluminaHiSeq2500",
				"Lane": "1",
				"Barcode": "ACGTAT"
			},
			"Adapter": "illumina"
		}
	],
	"Reference": {
		"GenomeInfo": "testdata/testReference/testReference.info.json",
		"Capture": "testCapture"
	},
	"Config": {
		"Threads": 4,
		"RemoveTempFiles": true
	}
}

Reference with GenomeInfo file and Captures can be prepared with exoclasma-index.

Call

exoclasma-pipe Call -u ${unit_json_file} -d ${dbSNP_vcf_gz}

Here you will need a Unit JSON file which was created with exoclasma-pipe Align. dbSNP will be used for BQSR stage.