fromer
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a7af1a164b
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Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-27 01:50:36 +00:00 |
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fromer
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c357ec775a
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Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4568 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-25 16:58:41 +00:00 |
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fromer
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9ba7269728
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Fixed Integration Tests to output VCF files with -NO_HEADER
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4548 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-21 19:49:44 +00:00 |
kshakir
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b88cfd2939
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Updated MD5s of VCFs, since the approximate command line arguments injected into the VCF headers now have a little more order to them thanks to changes in the ParsingEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4538 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-21 03:07:40 +00:00 |
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fromer
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f76865abbc
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ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4534 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-20 20:27:10 +00:00 |
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fromer
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bdd3a9752e
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Changed min MQ and BQ to 20 (for phasing)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4469 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-08 19:27:45 +00:00 |
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fromer
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ee00dcb79d
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1. Phasing now ignores bases without minimum base quality (BQ) and minimum mapping quality (MQ); 2. The probability of a non-called base is now divided by 3, to evenly split up the error probability over the non-called bases
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4450 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-07 17:40:59 +00:00 |
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fromer
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652a3e8de5
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Added integration tests for ReadBackedPhasing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4446 348d0f76-0448-11de-a6fe-93d51630548a
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2010-10-06 20:50:32 +00:00 |