Welcoming 2014 the best way I know...
I've aligned a good deal of illumina data I have accumulated in order to call SNPs with GATK. I had over looked the fact that some of the older runs are with the illumina 1.5 (phred+64) quality encoding. GATK does not like this. I would like to convert the BAM files to 1.9/sanger/phred+33 quality. Can anyone recommend a tool that would do this? If I have to do it to fastq files so be it... I will happily take recommendations for that conversion although there seems to be more options available.
Thank you and happy new year.
p.s. if there is a way to inform GATK that specific files have different encoding I am all ears.
I've aligned a good deal of illumina data I have accumulated in order to call SNPs with GATK. I had over looked the fact that some of the older runs are with the illumina 1.5 (phred+64) quality encoding. GATK does not like this. I would like to convert the BAM files to 1.9/sanger/phred+33 quality. Can anyone recommend a tool that would do this? If I have to do it to fastq files so be it... I will happily take recommendations for that conversion although there seems to be more options available.
Thank you and happy new year.
p.s. if there is a way to inform GATK that specific files have different encoding I am all ears.
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