Hey all,
I am attempting to use this for the first time. Here are my commands:
java -Xmx2000M -jar /Tools/GenomeAnalysisTK-1.0.2885/GenomeAnalysisTK.jar -T RealignerTargetCreator -R Path/hg18_reference_seq.fa -o Test_Output_File_21_Step1 -I Test_ID.21.bam
java -Xmx4000M -jar /Tools/GenomeAnalysisTK-1.0.2885/GenomeAnalysisTK.jar -T IndelRealigner -I Test_ID.21.bam -R Path/hg18_reference_seq.fa -targetIntervals Test_Output_File_21_Step1 -o Test_21_newAligned.bam
The first command runs fine. The second command gives this error:
The following error has occurred:
org.broadinstitute.sting.utils.StingException: First element of the alt consensus cigar must be M or I. Actual: 3H7M1D91M:
I'm pretty new to all of this. What is an "alt consensus cigar", and how should I go about trying to fix this? My first data set were a sample of 1 million paired end reads that I aligned with Novoalign, output in SAM format, sorted, removed duplicates using Picard, sorted, and then tried to do this.
I am attempting to use this for the first time. Here are my commands:
java -Xmx2000M -jar /Tools/GenomeAnalysisTK-1.0.2885/GenomeAnalysisTK.jar -T RealignerTargetCreator -R Path/hg18_reference_seq.fa -o Test_Output_File_21_Step1 -I Test_ID.21.bam
java -Xmx4000M -jar /Tools/GenomeAnalysisTK-1.0.2885/GenomeAnalysisTK.jar -T IndelRealigner -I Test_ID.21.bam -R Path/hg18_reference_seq.fa -targetIntervals Test_Output_File_21_Step1 -o Test_21_newAligned.bam
The first command runs fine. The second command gives this error:
The following error has occurred:
org.broadinstitute.sting.utils.StingException: First element of the alt consensus cigar must be M or I. Actual: 3H7M1D91M:
I'm pretty new to all of this. What is an "alt consensus cigar", and how should I go about trying to fix this? My first data set were a sample of 1 million paired end reads that I aligned with Novoalign, output in SAM format, sorted, removed duplicates using Picard, sorted, and then tried to do this.
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