480
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Usage
datfile : (-dname)
datfile : (-dname)
glfIndexFile : (-gname)
glfIndexFile : (-gname)
posterior cutoff : 0.500 (-c99.999)
posterior cutoff : 0.50 (-c99.999)
Additional Options
Additional Options
Alternative input file : --in_vcf []
Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04]
Scaled mutation rate : --theta [1.0e-03]
Prior of ts/tv ratio : --poly_tstv [2.00]
Prior of ts/tv ratio : --poly_tstv [2.00]
Non-autosome labels : --chrX [X], --chrY [Y], --MT [MT]
de novo mutation : --denovo, --rate_denovo [1.5e-08],
de novo mutation : --denovo, --rate_denovo [1.5e-08],
--tstv_denovo [2.00], --minLLR_denovo [1.00]
--tstv_denovo [2.00], --minLLR_denovo [0.01]
Optimization precision : --prec [1.0e-04]
Optimization precision : --prec [1.0e-04]
Multiple threading : --nthreads [1]
Multiple threading : --nthreads [1]
Filters : --minMapQuality, --minDepth, --maxDepth,
Output : --vcf [variantCalls.vcf], --gl_off
--minPercSampleWithData [0.00]
Output : --out_vcf [], --pos [], --all_sites, --gl_off,
--quick_call
