gatk-3.8

Author	SHA1	Message	Date
ebanks	bb312814a2	UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter). Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-16 17:28:09 +00:00
ebanks	31b1d60d28	Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2314 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-10 19:50:06 +00:00
ebanks	11ac7885b0	Pull out StratifiedAlignmentContext code so other walkers can use it. This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2312 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-10 19:21:16 +00:00

Author

SHA1

Message

Date

ebanks

UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter).

Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a

2009-12-16 17:28:09 +00:00

ebanks

31b1d60d28

Generalized the StratifiedAlignmentContext code so that it's easy to add new ways to stratify. Then added an MQ0-free stratification so we don't need to be carrying around 2 different alignment contexts (full vs. mq0-free) anymore.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2314 348d0f76-0448-11de-a6fe-93d51630548a

2009-12-10 19:50:06 +00:00

ebanks

11ac7885b0

Pull out StratifiedAlignmentContext code so other walkers can use it.

This is basically a wrapper class around AlignmentContext which allows you to stratify a context by e.g. reads on forward vs. reverse strands.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2312 348d0f76-0448-11de-a6fe-93d51630548a

2009-12-10 19:21:16 +00:00

3 Commits (f587ff46af8800fa70ca0408ca89bed635000a21)