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GATK 18.104.22.168 Variant Recalibrator ERROR
Could someone please provide me with a help to run Variant Recalibrator for GATK22.214.171.124？
when running the tool using GATK 126.96.36.199 with the following command line:
time ~/gatk-188.8.131.52/gatk VariantRecalibrator
-R ~/reference/hg19.fa -V ~/MT-1/outname.HC.vcf.gz
--use-annotation DP --use-annotation QD --use-annotation FS --use-annotation SOR --use-annotation ReadPosRankSum --use-annotation MQRankSum
--truth-sensitivity-tranche 100.0 --truth-sensitivity-tranche 99.9 --truth-sensitivity-tranche 99.0 --truth-sensitivity-tranche 95.0 --truth-sensitivity-tranche 90.0
I met this questiion: A USER ERROR has occurred: Couldn't read file file:///home/chenjie1/~/reference/hg19/hapmap_3.3.hg19.sites.vcf. Error was: It doesn't exist
The command syntax follows the same pattern as version 184.108.40.206.
Has the syntax been changed for GATK version 220.127.116.11?