Attention: Want an end-to-end pipelining solution for GATK Best Practices?
SplitNCigarReads complains about Badly form genome loc!
Dear GATK developers,
Thanks for this nice and practical tool with great supports! I tried to find relevant information in forum for this error reported by splitNCigarReads walker but couldn't find any information. So I hope I am not bulking the forum. Here is the error
MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:The stop position 69 is less than start 70 in contig JH375787.1
The same reference has been used as in previous steps for RG and MarkDup. I get this error for some of my samples not all.
It's the command if it can help:
java -jar /sw/apps/bioinfo/GATK/3.1.1//GenomeAnalysisTK.jar -T SplitNCigarReads -R /home/nimar/b2013097/private/nobackup/data/Reference/Reference.fa -I Sample_50T.merged.Reordered.sort.RG.MarkDup-filtered-unmapped.bam -U ALLOW_N_CIGAR_READS -o Sample_50T.merged.Reordered.sort.RG.MarkDup-filtered-unmapped.SplitN.bam
Looking forward to your comments