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edits
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The following parameters are in effect:
The following parameters are in effect:
pedfile : test.ped (-pname)
pedfile : (-pname)
datfile : test.dat (-dname)
datfile : (-dname)
glfIndexFile : test.gif (-gname)
glfIndexFile : (-gname)
posterior cutoff : 0.900 (-c99.999)
posterior cutoff : 0.500 (-c99.999)
Additional Options
Additional Options
Map Quality Filter : --minMapQuality
Map Quality Filter : --minMapQuality
Depth Filter : --minDepth [150], --maxDepth [200],
Depth Filter : --minDepth, --maxDepth,
--minPercSampleWithData [0.00]
--minPercSampleWithData [0.00]
Scaled mutation rate : --theta [1.0e-03]
Scaled mutation rate : --theta [1.0e-03]
Prior of ts/tv ratio : --tstv [2.00]
Prior of ts/tv ratio : --poly_tstv [2.00]
de novo mutation : --denovo, --rate_denovo [0.00],
de novo mutation : --denovo, --rate_denovo [1.5e-08],
--tstv_denovo [2.00], --minLLR_denovo [1.00]
--tstv_denovo [2.00], --minLLR_denovo [1.00]
Optimization precision : --prec [1.0e-04]
Optimization precision : --prec [1.0e-04]
Multiple threading : --nthreads [4]
Multiple threading : --nthreads [1]
Output : --vcf [test.vcf], --gl_off
Chromosomes to process : --chr2process []
Output : --vcf [variantCalls.vcf], --gl_off
