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Jump to navigationJump to searchPolymutt: a tool for calling polymorphism and de novo mutations in families for sequencing data (view source)
Revision as of 16:38, 11 February 2012
, 16:38, 11 February 2012no edit summary
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
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0'']
--tstv_denovo : the prior ts/tv ratio of ''de novo'' mutations. [''Default: 2.0'']
--minLLR_denovo : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0'']
--minLLR_denovo : minimum value of log10 likelihood ratio of allowing vs. disallowing ''de novo'' mutations in the data to output [''Default: 1.0'']
--chr2process: the chromosome names to process. If multiple chromosomes are provided, they should be separated by comma, e.g. --chr2process 2,10 or --chr2process chr2,chr10
--gl_off: not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations
--gl_off: not to output genotype likelihood values for each individual. Default is to output 3 GLs for polymorphisms and 10 GLs for de novo mutations
