Our staff will be observing the holiday and will be unavailable from 22nd to 25th November. This will cause a delay in reaching out to you and answering your questions immediately. Rest assured we will get back to it on Monday November 26th. We are grateful for your support and patience.
Have a great holiday everyone!!!
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?