Sanger and Illumina Fastq quality scores

cuscu

Hi, I use GATK for Variant Call in an Investigation Unit. When I use RealignerTargetCreator, I get an error: I'm using a wrong encoding for quiality scores. Which encoding (sanger, illumina, solexa) is ok to use with GATK? Do you have any tool to convert to that encoding? Thank you

Geraldine_VdAuwera

Please see the paragraph on quality score encodings here: http://www.broadinstitute.org/gatk/guide/article?id=1991

cuscu

Oh! Yes! Thanks. That's what I was looking for.