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VariantRecalibrator error using GATK bundle vcf files

Hi,

I'm using gatk-4.0.0.0 and I'm trying to call VariantRecalibrator

/opt/gatk-4.0.0.0/gatk VariantRecalibrator \
-R ${REF_GENOME} \
-V vcf/${SAMPLE_ID}.vcf.gz \
--resource hapmap,known=false,training=true,truth=true,prior=15.0:${VARIANCE_REFERENCE}/hapmap_3.3.b37.vcf.gz \
--resource omni,known=false,training=true,truth=false,prior=12.0:${VARIANCE_REFERENCE}/1000G_omni2.5.b37.vcf.gz \
--resource 1000G,known=false,training=true,truth=false,prior=10.0:${VARIANCE_REFERENCE}/1000G_phase1.snps.high_confidence.b37.vcf.gz \
--resource dbsnp,known=true,training=false,truth=false,prior=2.0:${VARIANCE_REFERENCE}/dbsnp_138.b37.vcf.gz \
-an DP \
-an QD \
-an FS \
-an SOR \
-an MQ \
-an MQRankSum \
-an ReadPosRankSum \
-an InbreedingCoeff \
-mode SNP \
-O recalibration/output.snp.recal \
--tranches-file recalibration/output.snp.tranches \
--rscript-file recalibration/output.snp.plots.R

I downloaded the reference vcf files from the GATK bundle but I got this error

A USER ERROR has occurred: Input /datos/nagen/gatk_resources/hapmap_3.3.b37.vcf.gz must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

the hapmap_3.3.b37.vcf.idx.gz is in the same folder than hapmap_3.3.b37.vcf.gz

when trying to index the file with IndexFeatureFile I got this error

A USER ERROR has occurred: File /datos/nagen/gatk_resources/hapmap_3.3.b37.vcf.gz is malformed: Input file is not in valid block compressed format., for input source: /datos/nagen/gatk_resources/hapmap_3.3.b37.vcf.gz caused by Input file is not in valid block compressed format., for input source: /datos/nagen/gatk_resources/hapmap_3.3.b37.vcf.gz

running /opt/gatk-4.0.0.0/gatk ValidateVariants -V /datos/nagen/gatk_resources/hapmap_3.3.b37.vcf.gz shows no problem

08:46:04.435 INFO ValidateVariants - Initializing engine
08:46:04.729 INFO FeatureManager - Using codec VCFCodec to read file file:///datos/nagen/gatk_resources/hapmap_3.3.b37.vcf.gz
08:46:04.743 INFO ValidateVariants - Done initializing engine
08:46:04.743 INFO ProgressMeter - Starting traversal
08:46:04.743 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
08:46:11.050 INFO ProgressMeter - X:155073731 0.1 4165754 39642385.4
08:46:11.050 INFO ProgressMeter - Traversal complete. Processed 4165754 total variants in 0.1 minutes.
08:46:11.050 INFO ValidateVariants - Shutting down engine

any ideas?

thans in advance for your help,

Alberto

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @alabarga
    Hi Alberto,

    Weird. Can you try unzipping the VCF and index and seeing if the tool runs?

    Also, which version of Java are you using? Can you try with the latest GATK version?

    Thanks,
    Sheila

  • mshrutimshruti Member

    Hi @Sheila,

    I was facing a similar problem when running BaseRecalibrator. “An index is required but was not found for file /share/PI/euan/apps/gatk/gatk_bundle_b37/dbsnp_138.b37.vcf.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.”
    I had copied the dbsnp_138.b37.vcf.gz file from GATK resource bundle ftp site -ftp://ftp.broadinstitute.org/bundle/b37/ along with the index files.

    Unzipping the VCFs and zipping them again with bgzip and later indexing with IndexFeatureFile resolved the issue.

  • SheilaSheila Broad InstituteMember, Broadie admin

    @mshruti
    Hi,

    Thanks for reporting your solution. Also, perhaps this thread will help.

    -Sheila

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