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

Hi,

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.

Thanks!

Mark