usng VarScan with phred score 64

[morangal]

hi All
i'm new in this NGS "neighborhood", and wondering ig anyone can guide me on how to use the variant calling in VarScan with seq data that comes with Phred score of 64 ?
according to their documentation the software works with sanger scores (phred33), so i have to make the adjusment myself.
any help will be appreciated :-)

Moran

[maubp]

I'm not familiar with VarScan, but if it doesn't understand the (outdated) Illumina FASTQ files using PHRED with an offset of 64, then you must convert your FASTQ to the Sanger convention (PHRED with an offset of 33). There are several tools for this, e.g. EMBOSS seqret. See this thread (and others):

http://seqanswers.com/forums/showthread.php?t=5210