Rod span is not contained within the data shard...

zugzugzugzug Member ✭✭
edited September 2014 in Ask the GATK team


We ran HaplotypeCaller on some bams and got the same error on them: Rod span is not contained within the data shard, meaning we wouldn't get all of the data we need.

Here is my command:
java -Xmx32g -jar ~/GATK-3.2.2/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -R /hg19/hg19.fasta \ -I $1 \ -ERC GVCF \ -nct 16 \ --variant_index_type LINEAR \ --variant_index_parameter 128000 \ --pair_hmm_implementation VECTOR_LOGLESS_CACHING \ -o ${TEMPORARY_DIR}/$2

Can you help me figure out whats wrong? The error said it may be a bug and I cannot find where this issue was previously addressed. I wonder if something went wrong with the bam processing.

We received these bams from the sequencing institution already aligned. Individual reads were missing the @RG tag, so we used bamaddrg to add the @RG tags. That caused issues with the bam 'bins', so we had to run the htsjdk.samtools.FixBAMFile. We ran MarkDuplicates and attempted the above HaplotypeCaller command.



Post edited by zugzug on


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