iseq

iseq is an integrated analysis toolkit and pipeline for NGS panel sequencing data. If you have any question about this tool, please contact us.

Python class of iseq: ReffaFile, FastqFile, BamFile, SamFile, VcfFile, CsvFile, MpileupFile and ResultFile.

Processor of iseq: preprocess, variantcaller, refinement

Pipeline: panel, panel_somatic

Feature

• Multiple sequence alignment softwares
• Multiple variantion detection softwares
• Easy to use
• Extend easily
• Single configuration file do all things
• Output log be divided into in individual file

Install

source code

# Download the source code and gunzip
./install.R

Usage

configuration file is an important file to run iseq. Three type of parameters can be found in this file:

• tools
• extra files
• non-file type parameters

Tools: Command line tools, class of iseq can use these tools by self.cfg, e.g self.cfg["gatk"] (Need to download and install)

Extra files: Some of files required to run tools (Need to download)

Non-file type parameters: Other parameters (Do not need to download anything)

Germline Mode

# fastq2vcf mode
panel -c config.cfg \
         -s A01A \
         -m fastq2vcf \
         -1 A01A_1.fq.gz \
         -2 A01A_2.fq.gz \
         --bamprocess 00101111 \
         -o outdir

# fastq2bam
panel -c config.cfg \
         -s A01A \
         -m fastq2bam \
         -1 A01A_1.fq.gz \
         -2 A01A_2.fq.gz \
         --bamprocess 00101111 \
         -o outdir

# bam2vcf
panel -c config.cfg \
         -s A01A \
         -m bam2vcf \
         --in_bam A01A.bam \
         --bamprocess 00000000 \
         -o outdir

# genomeindex mode
panel -c config.cfg -m genomeindex

Somatic Mode

# fastq2vcf mode
panel_somatic -c config.cfg \
                 -s A01 \
                 -m fastq2vcf \
                 -1 A01A_1.fq.gz \
                 -2 A01A_2.fq.gz \
                 -3 A01C_1.fq.gz \
                 -4 A01C_2.fq.gz \
                 --bamprocess 00101111 \
                 -o outdir

# fastq2bam mode
panel_somatic -c config.cfg \
                 -s A01 \
                 -m fastq2bam \
                 -1 A01A_1.fq.gz \
                 -2 A01A_2.fq.gz \
                 -3 A01C_1.fq.gz \
                 -4 A01C_2.fq.gz \
                 --bamprocess 00101111 \
                 -o outdir

# bam2vcf mode
panel_somatic -c config.cfg \
                 -s A01 \
                 -m bam2vcf \
                 --case_in_bam A01A.bam \
                 --control_in_bam A01C.bam \
                 --bamprocess 00000000 \
                 -o outdir

# genomeindex mode
panel_somatic -c config.cfg -m genomeindex