Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

ERROR:The requested extended must fully contain the requested span

I got this error when running HaplotypeCaller:

ERROR MESSAGE: The requested extended must fully contain the requested span

My command is:
java -Xmx4g -jar ~/GATK_3.2/GenomeAnalysisTK.jar -T HaplotypeCaller -R ucsc.hg19.fasta -I Sample_55348_recal.bam --dbsnp dbsnp_138.hg19.vcf -L capture_targets_buffered10bases.bed --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 -o Sample_55348_rawcall_HCgvcf.vcf

What does the error mean?

Tagged:

Answers

Sign In or Register to comment.