I am trying to mine SNPs using Star 2-pass / GATK using the process outlined here.
I've run the two passes of STAR, but I'm getting an error during the picard processing step.
When I run this command;
java -jar /home/XXXXXX/XXXX/bin/picard.jar AddOrReplaceReadGroups I=Aligned.out.sam O=rg_added_sorted.bam SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample
I get the following error:
Exception in thread "main" java.lang.IllegalArgumentException: Cigar element being constructed with negative length: -65 and operation: D
Any ideas where I'm going wrong?