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I am trying to follow the best practices for mapping my (Paired-end Illumina HiSeq) reads to the reference, by following this presentation:
From what I understand, I should use MergeBamAlignment to clean up the output from bwa, and then use this cleaned up output for the rest of the analysis. However, when I run ValidateSamFile after running MergeBamAlignment I get a lot of errors, and running CleanSam on the file does not resolve any of them. What am I doing wrong? I've tried searching the web for more details about MergeBamAlignment but I haven't been able to find much. Please let me know if you require any additional information.
How I ran MergeBamAlignment
picard-tools MergeBamAlignment \
PAIRED_RUN=true # Why is this needed?
Error report from ValidateSamFile
## HISTOGRAM java.lang.String
Error Type Count