Arguments
homref.limits
lower limit, upper limit, number of homozygous reference
het.limits
lower limit, upper limit, number of heterozygous calls
homvar.limits
lower limit, upper limit, number of homozygous alternative
count.limits
lower limit, upper limit, total number of counts
percenthets.limits
lower limit, upper limit, Number of Heterozgyous / (Total Number of Counts) or percent het
titv.noncoding.limits
lower limit, upper limit, Transition transversion ratio in noncoding regions
titv.coding.limits
lower limit, upper limit, Transition transversion ratio in coding regions
readdepth.target
The sequencing depth target (eg 30x)
readdepth.limits
lower limit, upper limit, Mean read depth
readdepth.percent.limits
lower limit, upper limit, Percent read depth in target (50 percent to 200 percent of target read depth)
gq.limit
lower limit, Mean genotype quality (does not make sense to have an upper limit)
masked.limits
lower limit, upper limit, (Number of heterozygous in masked regions)/(Total number of heterozygotes)
non.masked.limits
lower limit, upper limit, (Number of heterozygous in non-self chained regions)/(Total number of heterozygotes)
het.gap.limits
lower limit, upper limit, Largest gap within chromosome between two heterozygous calls
gq.filter
filter for the VCF file on genotype quality (eg only GQ > 90)
dp.filter
filter for the VCF file on read depth (eg only DP > 0)