I am trying to get bam file metrics and for this i am using gatk CollectAlignmentSummaryMetrics command. My code is as following
gatk CollectAlignmentSummaryMetrics -R hg19.fa -I RG.bam -O bammetrics.txt
my hg19.dict file is also in the same folder as the rest of the files mentioned above. I also created my dict file from unzipped reference file.
I am getting the error SequenceUtil$SequenceListsDifferException: Sequences at index 1 don't match: 1/135534747/chr10 1/243199373/chr2/M5=a0d9851da00400dec1098a9255ac712e/UR=file:hg19.fa
Can any one please tell me what this error means and how to fix it.
Thanks in advance.