kiran
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84ddadca64
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One more fix: exclude input VCF file's directory name from the output file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4226 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-08 03:09:08 +00:00 |
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kiran
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bd878565f6
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Change for Firehose: infers output path from the input VCF, so that we don't have to change a whole bunch of stuff so that Firehose knows where to expect the output file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4221 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-07 21:07:46 +00:00 |
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kiran
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e9af893bf4
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Write headers that are VCF4.0 compliant
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4213 348d0f76-0448-11de-a6fe-93d51630548a
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2010-09-03 23:46:27 +00:00 |
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kiran
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1c3f2be829
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Change for Chris: don't depend on other Perl modules.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4053 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-17 22:19:13 +00:00 |
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kiran
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23b5d71e76
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A quickly hacked together replacement for AnnotateVCFwithMAF.py, which doesn't work anymore with Cancer's updated annotator. Takes an annotated MAF file and imports the annotations into the VCF file. For the MAF annotator's DNP and TNP annotations (which I think are likely to not be correct, given the lack of phasing information or even proper association to the same sample), just propagate the annotation from the previous annotated variant to which the multinucleotide polymorphism was associated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4007 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-11 00:20:08 +00:00 |