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
# Download the source code and gunzip ./install.R
configuration file is an important file to run iseq. Three type of parameters can be found in this file:
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)
# 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
# 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
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