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Q: Does --mle overwrite fed-in genotypes?<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: Does --mle overwrite fed-in genotypes?<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 <br>
Q: How do I get reference files for an region of interest? <br>
A: (1) For HapMapII format, download http://www.sph.umich.edu/csg/ylwtx/HapMapForMach.tgz <br>
For MACH format, you can do the following:
(2) 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.
(2-1) First, find the first and last SNP in the region you are interested in. Say "rsFIRST" and "rsLAST", defined according to position.
Then:
(2-2) Then:
@ first = `grep -n rsFIRST orig.snps | cut -f1 -d ':'`
@ first = `grep -n rsFIRST orig.snps | cut -f1 -d ':'`
@ last = `grep -n rsLAST 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):
(2-3) 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
awk '{print $3}' orig.hap | cut -c${first}-${last} > region.hap
