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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 |
| + | |
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| --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 |