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Input files reads and reference have incompatible contigs
Dear GATK team,
I'm re-running an analysis pipeline with the new GATK version 3.5 on human samples. I have already analyzed my data with the older 3.1 version without any problems.
I am having troubles now with the IndelRealigner step.
ERROR MESSAGE: Input files reads and reference have incompatible contigs. Please see http://gatkforums.broadinstitute.org/discussion/63/input-files-have-incompatible-contigsfor more informa
tion. Error details: Found contigs with the same name but different lengths or MD5s:
ERROR contig reads is named chr20 with length 63025520 and MD5 0dec9660ec1efaaf33281c0d5ea2560f
ERROR contig reference is named chr20 with length 63025520 and MD5 1ef908e47ac040f0e94ede396c59f074.
ERROR reads contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]
ERROR reference contigs = [chrM, chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY]
This happens for all my samples.
The reason I am re-running all these steps is because I want to use the HC in GVCF mode and this was not possible with my older GATK version. I didn't want to mix versions so I started the whole pipeline again. Is this really necesary? Or can I just do the HC in GVCF mode on the 3.1 generated bam files?
Thanks a lot!!