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GenotypeGVCF ERROR: An index is required, but none found., for input source: FileName.gvcf.gz

wolfemdwolfemd TheUniverseMember

Hi there,

I have a gVCF file provided from another research group. It contains ~60 whole genomes supposedly output by the HaplotypeCaller at BP_RESOLUTION. I have a set of SNPs in a VCF for about 700 individuals, generated by a separate group. I want to subset the gVCF samples to just the loci represented in the VCF, regardless of whether they are variant in that set or not and compare the SNP-typed set of 700 with the whole genome-sequenced set. I tried the following:

java -Xms2g -Xmx9g -jar GenomeAnalysisTK.jar \
--analysis_type GenotypeGVCFs \
--reference_sequence ReferenceGenome.fa \
--variant FileName.gvcf.gz \
--intervals chr1.vcf \
--out SubsetSites_chr1.vcf.gz

I get the error: ERROR: An index is required, but none found., for input source: FileName.gvcf.gz

Perhaps the index file (.tbi?) was originally output by GATK but is not provided to me. What can I do? Or am I doing something obviously wrong? I am new to GATK.

Thanks in advance!

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