From Genome Analysis Wiki
Jump to navigationJump to search
5 bytes added
, 15:35, 20 May 2010
Line 115: |
Line 115: |
| A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout: | | A: A simple approach is to use --mask option. For example, --mask 0.02 masks 2% of the genotypes at random, impute them and compare with the masked original to estimate genotypic and allelic error rates. Messages like the following will be generated to stdout: |
| | | |
− | Comparing 948352 masked genotypes with MLE estimates ...<br> Estimated per genotype error rate is 0.0568<br> Estimated per allele error rate is 0.0293<br><br> | + | Comparing 948352 masked genotypes with MLE estimates ...<br> Estimated per genotype error rate is 0.0568<br> Estimated per allele error rate is 0.0293<br><br> |
| | | |
| <br> | | <br> |
Line 134: |
Line 134: |
| awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap | | awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap |
| | | |
− | <br>'''Q: Do I have to sort the pedigree file by physical positions? '''<br> A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br> | + | <br>'''Q: Do I have to sort the pedigree file by physical positions? '''<br> A: If you use external reference, you do not have to as long as the external reference is in correct order. **HOWEVER**, we strongly recommend sorting the pedigree files. <br><br> |
| | | |
| <br>'''Q: What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''<br> A: mach automatically resets it to maximum possible value. | | <br>'''Q: What if I specified --states R where R exceeds the maximum possible (2*number diploid individuals - 2 + number_haplotypes)? '''<br> A: mach automatically resets it to maximum possible value. |
| | | |
− | <br> | + | <br> |
| | | |
| '''Q: Can I used unphased reference?'''<br> | | '''Q: Can I used unphased reference?'''<br> |