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55 bytes added
, 18:24, 18 June 2011
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| The following parameters are in effect: | | The following parameters are in effect: |
− | pedfile : (-pname) | + | pedfile : test.ped (-pname) |
− | datfile : (-dname) | + | datfile : test.dat (-dname) |
− | glfIndexFile : (-gname)
| + | glfIndexFile : test.gif (-gname) |
− | cutoff : 0.500 (-c99.999)
| + | posterior cutoff : 0.900 (-c99.999) |
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| Additional Options | | Additional Options |
| Map Quality Filter : --minMapQuality | | Map Quality Filter : --minMapQuality |
− | Depth Filter : --minDepth, --maxDepth, | + | Depth Filter : --minDepth [150], --maxDepth [200], |
| --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] |
| + | de novo mutation : --denovo, --denovo_rate [0.00], |
| + | --denovo_tstv [0.50], --denovo_min_LLR [1.00] |
| Optimization precision : --prec [1.0e-04] | | Optimization precision : --prec [1.0e-04] |
− | de novo mutation : --denovo, --rate_denovo [0.00],
| + | Multiple threading : --nthreads [4] |
− | --tstv_denovo [0.50], --min_denovo_LLR [0.00]
| + | Output : --vcf [test.vcf], --gl_off |
− | Output : --vcf [variantCalls.vcf] | |
− | Multiple threading : --nthreads [1]
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