Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
Input files reads and reference have incompatible contigs while Running GATK:RealignerTargetCreator
I am running RealignerTargetCreator using GATK version GenomeAnalysisTK-1.2-4-gd9ea764 and I am getting the following error:
ERROR MESSAGE: Input files reads and reference have incompatible contigs: Found contigs with the same name but different lengths:
ERROR contig reads = scaffold69676_size1796 / 3149
ERROR contig reference = scaffold69676_size1796 / 1758.
ERROR reads contigs = [scaffold1_size320545, scaffold2_size291774, scaffold3_size284740..........`
I already checked that I am using the right Reference FASTA file and the correct .bam file, that I have used for alignment before. Therefore, I am clueless why I am getting this error?
I would appreciate your help regarding this problem. Any suggestion is welcome?