gatk-3.8

Commit Graph

Author	SHA1	Message	Date
ebanks	9b2fcc4711	Refactoring of the annotation system: 1. VA is now a ROD walker so it no longer requires reads (needs a little more testing) 2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs) 3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong. Fixed the headers too. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a	2010-06-09 17:05:51 +00:00
delangel	355396109b	Bug fix to avoid build failure (class changed under me??) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3416 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-21 18:48:56 +00:00
delangel	1753d07b02	Added AnnotationByAlleleFrequencyWalker - walker takes an input vcf, a reference vcf and a list of annotations (with the -A argument). For each site present in both VCF's, it outputs the given annotations into the screen as well as allele frequency. Since HapMap vcf reference doesn't include AF in annotations, it computes it from Chromosome, Het and HomVar counts. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3415 348d0f76-0448-11de-a6fe-93d51630548a	2010-05-21 18:31:34 +00:00

Author

SHA1

Message

Date

ebanks

9b2fcc4711

Refactoring of the annotation system:

1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong.  Fixed the headers too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a

2010-06-09 17:05:51 +00:00

delangel

355396109b

Bug fix to avoid build failure (class changed under me??)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3416 348d0f76-0448-11de-a6fe-93d51630548a

2010-05-21 18:48:56 +00:00

delangel

1753d07b02

Added AnnotationByAlleleFrequencyWalker - walker takes an input vcf, a reference vcf and a list of annotations (with the -A argument). For each site present in both VCF's, it outputs the given annotations into the screen as well as allele frequency. Since HapMap vcf reference doesn't include AF in annotations, it computes it from Chromosome, Het and HomVar counts.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3415 348d0f76-0448-11de-a6fe-93d51630548a

2010-05-21 18:31:34 +00:00

3 Commits (b21f90aee0678e550746e101c6d0629ca962bce6)