Tophat, Cufflinks and SamTools - Bioinformatics in BioMed

 

Converter for vcf to bed format - SEQanswers

sed -e 's/chr//' file.vcf | awk '{OFS="\t"; if (!/^#/){print $1,$2-1,$2,$4"/"$5,"+"}}'

Bioinformatics software and tools

bamtools:
API and toolkit for reading, writing, and manipulating BAM (genome alignment) files
http://github.com/pezmaster31/bamtools/

bedtools:
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.
http://code.google.com/p/bedtools/