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Error stack trace Error Message: For input string: "R"
Hi, I've run Samtools1.0 & bcftools1.0 which output vcf4.2 which caused issuse. So I've updated to the latest version of GATK & am now getting this Error which I cannot resolve.
Program Args: --variant SPARK.common.vcf -R Documents/RefSeqIndexAllPrograms/GATK/hg19_1stM_unmask_ran_all.fa -T SelectVariants -o 24999.SPARK.common.vcf -sn 24999 -env -nt 4
ERROR stack trace
java.lang.NumberFormatException: For input string: "R"
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
ERROR MESSAGE: For input string: "R"
Any help would be gratefully received.