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Selec a fraction of variants of a specific chromosome
I am using the following expression to select variants from my VCF file:
java -jar GenomeAnalysisTK.jar \
-T SelectVariants \
-R reference.fasta \
-V input.vcf \
-o output.vcf \
I am wondering if the expression above will extract the 50% of variants of the chromosome_x or will extract the 50% of all the variants in the VCF and then it will print those that fall in the chromosome_x . I suspect the first behaviour is the correct (it is what I need), but I am asking to be sure.
Thanks in advance,