When using MPileup I received an error in that all the output was for chr10 (even when my file only contained info for chr20), the ALT position was always X, and the quality score was 0. Therefore for some reason the variant calling failed but I don't know why. Can anyone help?
The input fastq sequence quality is very, very low. It may not be usable. Run FastQC to review.
The quality impacts mapping (very few sequences map at all) plus all downstream steps. GATK tools failing is a known - these are deprecated and not recommended. Alternative variant detection methods are covered in the tutorials.
Thanks, Jen, Galaxy team