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SelectVariants doesn't appear to work on Haploid VCFs
I am still working on how to process sex-chromosomes correctly, and as a result I have a VCF of haploid calls for a few hundred male X-chromosomes. I am trying to subset out by sample using SelectVariants, but it throws the following error:
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4): ... ##### ERROR MESSAGE: All samples must be diploid
The relevant part of the command is the following:
java -Xmx8g -Djava.io.tmpdir=$TMPDIR -jar /apps/GATK/3.5/GenomeAnalysisTK.jar \ -T SelectVariants \ --sample_file Final385Samples.219males.list \ --excludeNonVariants \ --removeUnusedAlternates \ -R /project/production/Indexes/samtools/hsapiens.hs37d5.fasta \ -V 312Samples.ChrX.haploid.vcf.gz \ -o 219samples.ChrX.haploid.vcf.gz
I tried running with version 3.4, which doesn't seem to complain about this issue, however it is not happy with the "*" alleles.
Is there any simple workaround for this that will provide a correctly formatted output file, or am I doing something wrong?