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A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.<br><br>
A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.<br><br>
Q: How do I get reference files for an region of interest? <br>
A: For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz
For MACH format, you can do the following:
First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.
Then:
@ first = `grep -n rsFIRST orig.snps | cut -f1 -d ':'`
@ last = `grep -n rsLAST orig.snps | cut -f1 -d ':'`
Finally (assuming the third field contains the actual haplotypes, where alleles are separated by nothing):
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
== Examples ==
== Examples ==
