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Software Utilities

These software utilities were created at the University of Washington for research purposes. The scripts offered here are provided “as is” with no guarantee of performance or support, or completeness of documentation. Academic researchers are encouraged to freely use and modify them for research applications.

RunGATK.py A utility for calling variants with the Broad Genome Analysis Toolkit
RunBowtie.py A utility for running Bowtie, a Burrows-Wheeler aligner
FilterFastq2Fastq.pl A utility for filtering sequencer reads based on quality
FilterFastq2Fasta.pl A utility for filtering sequencer reads based on quality
ExtractBAMPositionCounts.py

A utility for counting the number of reads mapping to all reference positions in a BAM alignment file
RNA-Seq-1.1.tar.gz

A set of scripts for counting and annotating RNA-Seq data