I used GATK UnifiedGenotyper (latest build) to call variants.
Now I have a vcf-file which I want to filter. Although the corresponding fields are correctly defined in the header:
##fileformat=VCFv4.1
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
I always get an "undefined variable" error when I filter for MQRankSum or ReadPosRankSum .
Any suggestions are very welcome!
Now I have a vcf-file which I want to filter. Although the corresponding fields are correctly defined in the header:
##fileformat=VCFv4.1
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
I always get an "undefined variable" error when I filter for MQRankSum or ReadPosRankSum .
Any suggestions are very welcome!
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