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HaploShare: identification of extended haplotypes shared by cases and evaluation against controls

Dingge Ying

Recent founder mutations may play important roles in complex diseases and Mendelian disorders. Detecting shared haplotypes that are identical by descent (IBD) could facilitate discovery of these mutations. Several programs address this, but are usually limited to detecting pair-wise shared haplotypes and not providing a comparison of cases and controls. We present a novel algorithm and software package, HaploShare, that detects extended haplotypes that are shared by multiple individuals, and allows comparisons between cases and controls. Testing on simulated and real cases demonstrates significant improvements in detection power and reduction of false positive rate by HaploShare relative to other programs.

Files (49.4 MB)
Name Size
300test.map
md5:c2d1fe7f727b24fa4742b13c13f85e1d
969.1 kB Download
300test.ped
md5:61304b3ce997dad1902ffa0c4139032f
47.1 MB Download
gitattributes.txt
md5:90d90ea9b5f5dbce1894d4d7e7c8a50c
395 Bytes Download
gitignore.txt
md5:ff60c06619fec7ae7fe197a282cf30b1
617 Bytes Download
HaploShare.exe
md5:bcfbf773acbf1ca40acf3137895d5801
51.7 kB Download
newhap_freq_chr1.txt
md5:a5e9096b4d185041b75c8f34444ce31e
1.3 MB Download
PhasedToBlockFreq.exe
md5:1ff7bc5d5c0e5e3c784a5268f03b577f
13.8 kB Download
sample_output.txt
md5:cf0228b39ec5943bf5728d9e7e8465f5
1.9 kB Download
to22.pl
md5:860d56d00e932f8282e1442263886414
546 Bytes Download
UserGuide.txt
md5:73dea015a2a936d764e758850b789363
2.8 kB Download
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