Entering edit mode
9.8 years ago
nilakshafreezon
▴
120
Hi, I am successfully using my GATK variant calling pipeline for exome sequence data, and got this error when I tried to call variants from a pretty much old genome sequence (back in 2009) which was stored in our computers with no analysis being done for ages.
SAM/BAM file SAMFileReader{/scratch/3041404/P394_102.prmdup.bam} appears to be using the <n/>wrong encoding for quality scores: we encountered an extremely high quality score </n>
of 70; please see the GATK --help documentation for options related to this error
This should be becuase of the Illumina Encodings have been changed from time to time. And my old sequences are from some older encoding version. Is there any possible way to check my exact illumina/Solexxa pipeline version and a way /software to uplift the quality encodings so that I can run it through GATK without any hassle.
Thank you in advance.
