Using the seqtool
script¶
Overview¶
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
-i INDEXFILE, --indexFile INDEXFILE
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 PATEEM_DNA.snp_fixed.final.vcf.gz -o PATEEM_DNA.snp_fixed.final.txt