CombineVariants_ERROR
Posted in Ask the GATK team | Last updated on 2013-01-14 14:20:02


Comments (4)

Hi. I want to merge two VCF files. Initially I was selected only indels(by select variant option). Now I want to merge these two VCF file which contains only INDELS. But When I run the command, I am getting the same error:

ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace 
java.lang.NumberFormatException: For input string: "."

I run this command:

java -jar -Xmx2g GenomeAnalysisTK.jar -R hg19_5.fasta -T CombineVariants -V indelsample1.vcf -V indelsample3.vcf -o indels1s3.vcf -genotypeMergeOptions UNIQUIFY

Could you please tell me what is the reason behind this? and how to merge two VCF file having INDELS?

Thanks in advance.


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