cannot use SelectVariants to combine VCF files

I try to use SelectVariants to find concordance between two VCF files, one generated from GATK UnifiedGenotyper and the other from samtools mplieup.
But I get error message showing the samtools VCF file malformed, which I found caused by heterozygous sites in indel (e.g., R, Y, W, M, S or W in indel sequence ).
Is there a way to bypass this problem when using GATK SelectVaraints?

Thanks,

Chih-Ming