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SelectVariants --removeUnusedAlternates option not working

nell_morgannell_morgan Curtin University, Perth, Western AustraliaMember

Dear GATK team,

I am using GATK version 3.2-2 and am trying to process a vcf file with SelectVariants to remove variant calls where the sample is homozygous for the reference allele. I have a joint genotyped vcf with two samples, but have separated these into two separate vcfs. Now I want to remove instances where the sample does not have the called snp/indel. The format of the command that I tried is:
java -jar GenomeAnalysisTK.jar \
-T SelectVariants \
-R reference.fasta \
-V input.vcf \
-o output.vcf \
--removeUnusedAlternates

I get an error message: 'Argument with name 'removeUnusedAlternates' isn't defined. Any advice as to why the option is not working would be appreciated. I also tried '-trimAlternates true' but this didn't work either.

Basically what I am trying to achieve is to generate fasta sequences that are representative of the samples using FastaAlternateReferenceMaker. But this program seems to output the alternate base regardless of the genotype of the sample.

Thank you!

Answers

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