GATK GenomicsDBImport intervals
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10 months ago
MAPK ★ 1.7k

I am tryiing to run GenomicsDBImport for exome region of chromosome 2 for whole genome gvcf (multiple samples provided as mylist2.list)

my bed file is in this format:

chr2.bed

chr2    41359   41765
chr2    45307   45927
chr2    45729   46454

mylist2.list

1_S    /544562991/1_S.chr2.g.vcf.gz
2_S    /544562991/2_S.chr2.g.vcf.gz

After running this command:

gatk --java-options "-Xms4G -Xmx32G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
 GenomicsDBImport \
--genomicsdb-workspace-path /home/exomes/SNPs/chr2 \
--batch-size 50 \
--intervals /08-JointCalling/SNPs/chr2.bed \
--sample-name-map /home/mylist2.list \
--tmp-dir=/data/tmp \
--reader-threads 5

I am getting this error below. Can someone please help me understand/resolve this error? org.broadinstitute.hellbender.exceptions.GATKException: Cannot call query with different interval, expected:chr2:41360-41765 queried with: chr2:45308-46454

GATK gvcf • 1.1k views
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I remember at one time GATK GenomicsDBImport did not allow multiple intervals. It seems now this problem has been fixed. See: https://gatkforums.broadinstitute.org/gatk/discussion/13447/genomicsdbimport-intervals. Can you check your GATK version?

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Yes that was version issue. It worked on GATK 4.1.7.0. Thanks!

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