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Test-drive the GATK tools and Best Practices pipelines on Terra

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RemoveAlternates not working on haploid VCFs

I'm getting an error on the latest version of SelectVariants when I try and remove alternate alleles in a haploid organism. If I remove the 'TrimAlternates' flag it works correctly, but obviously then I'm left with ghost alleles. Can't see any reason why all alleles should need to be diploid for this?



sredmond$ java -jar /humgen/gsa-hpprojects/GATK/bin/GenomeAnalysisTK-3.5-0-g36282e4/GenomeAnalysisTK.jar -R /seq/plasmodium/sredmond//refs/Pf3D7_v3.fasta -T SelectVariants -V 3D7DD2_300100.VQSR.Pass90.vcf -o 3D7DD2_300100.VQSR.Pass90.SM-7LV8U.vcf -sn SM-7LV8U -env -trimAlternates
Picked up _JAVA_OPTIONS: -Xmx8g -Xms1g
INFO 12:31:30,195 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:31:30,198 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56

ERROR MESSAGE: All samples must be diploid
ERROR ------------------------------------------------------------------------------------------


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