gatk-3.8

Author	SHA1	Message	Date
carneiro	e7d38247bb	chunkIntervals.lua creates 1Mb interval chunks out of any .intervals file. Useful for methods development pipeline datasets. remapAmplicons.lua takes a sam file with reads aligned to amplicon references, a reference genome , and an amplicon reference mapping table, and rewrites the sam file with mappings to the reference sequence. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-11 18:21:31 +00:00
carneiro	aab0ec209b	small bug fix on chromosome names. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5168 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-01 20:55:19 +00:00
carneiro	a2e2a6a9c3	A script to convert an intervals file into a sorted unoverlapping intervals file. Super fast implementation using multiple hashes, should do the job instantly no matter how big the intervals are. ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals file fixed before we can run Unified Genotyper because of scatter-gather. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5117 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-28 21:46:41 +00:00

Author

SHA1

Message

Date

carneiro

chunkIntervals.lua creates 1Mb interval chunks out of any .intervals file. Useful for methods development pipeline datasets.

remapAmplicons.lua takes a sam file with reads aligned to amplicon references, a reference genome , and an amplicon reference mapping table, and rewrites the sam file with mappings to the reference sequence.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-11 18:21:31 +00:00

carneiro

aab0ec209b

small bug fix on chromosome names.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5168 348d0f76-0448-11de-a6fe-93d51630548a

2011-02-01 20:55:19 +00:00

carneiro

a2e2a6a9c3

A script to convert an intervals file into a sorted unoverlapping intervals file. Super fast implementation using multiple hashes, should do the job instantly no matter how big the intervals are.

ps: this utility is similar to -im on GATK, but for queue scripts we need the intervals file fixed before we can run Unified Genotyper because of scatter-gather.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5117 348d0f76-0448-11de-a6fe-93d51630548a

2011-01-28 21:46:41 +00:00

3 Commits (e7d38247bbf068a3cd3c5679ac7aa0453291e1ad)