From Genome Analysis Wiki
Jump to navigationJump to search
107 bytes added
, 11:26, 8 October 2012
Line 28: |
Line 28: |
| datfile : (-dname) | | datfile : (-dname) |
| glfIndexFile : (-gname) | | glfIndexFile : (-gname) |
− | posterior cutoff : 0.500 (-c99.999) | + | posterior cutoff : 0.50 (-c99.999) |
| | | |
| Additional Options | | Additional Options |
− | Map Quality Filter : --minMapQuality
| + | Alternative input file : --in_vcf [] |
− | Depth Filter : --minDepth, --maxDepth,
| + | Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04] |
− | --minPercSampleWithData [0.00]
| |
− | 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] |
− | Chromosomes to process : --chr2process []
| + | Filters : --minMapQuality, --minDepth, --maxDepth, |
− | Output : --vcf [variantCalls.vcf], --gl_off | + | --minPercSampleWithData [0.00] |
− | | + | Output : --out_vcf [], --pos [], --all_sites, --gl_off, |
| + | --quick_call |
| | | |
| | | |