Using the seqtool script


The seqtools script is the entry point for command-line-oriented interaction with seqtools. Usage is pretty straightforward. To get top-level help, simply type:

seqtool -h

Usage Examples

Demultiplexing FastQ Files

$ seqtool utils demultiplex -h

This will return the help for the demultiplexer.

usage: seqtool utils demultiplex [-h] [-1 READFILE1] [-2 READFILE2]
                                 [-i INDEXFILE] [-j INDEXFILE2] [-x INDEX]

optional arguments:
  -h, --help            show this help message and exit
  -1 READFILE1, --readFile1 READFILE1
                        read1 filename
  -2 READFILE2, --readFile2 READFILE2
                        read2 filename
                        index Filename
  -j INDEXFILE2, --indexFile2 INDEXFILE2
                        index Filename
  -x INDEX, --index INDEX
                        The indexes, one per index or comma-separated pairs
                        for dual-barcode indexing

Fixing VarScan VCF Files

$ seqtool varscan fixVcf -h
usage: seqtool varscan fixVcf [-h] [-f VARSCAN]

optional arguments:
  -h, --help            show this help message and exit
  -f VARSCAN, --varscan VARSCAN
                        Filename of varscan VCF file [default=stdin]

Melt a VCF File to Tab-Delimited Text

A seqtool vcf subcommand, melt, can take a VCF file (including multisample VCFs) and output a tab-delimited text file, expanding all the various INFO and FORMAT columns as well as the snpEff output. For snpEff, note that the highest impact variant is chosen (based on the snpEff classification scheme.

$ seqtool vcf melt -f -o