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VCF input and BaseRecalibrator error

AmandaChamberlainAmandaChamberlain Agriculture VictoriaMember

I'm trying to run BaseRecalibrator with GATK4-Alpha. I'm using --knownSites to input a vcf file as follows:

java -Xmx80G -jar $GATK BaseRecalibrator \
-R reference.fa \
-I ${SAMPLE}_dedup.bam \
-knownSites KnownVariants.vcf \
-BQSR recal.table \
-O after_recal.table

However it returns the following error

A USER ERROR has occurred: Cannot read KnownVariants.vcf because no suitable codecs found

I've used this input file with GATK3.5.0 and it was fine.

Any guidance on what the problem might be would be much appreciated.


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