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gatk3的最后一个经典版本3.8
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Khalid Shakir 1808c90d2a Added introductory CRAM support. 
Replaced usage of GATKSamRecordFactory with calls to wrapper GATKSAMRecord extending SAMRecord.
Minor other updates for test changes.
Added exampleCRAM.cram generated by GATK, with .bai and .crai indexes generated by CRAMTools.
CRAM-to-CRAM test disabled due to https://github.com/samtools/htsjdk/issues/148
Using exampleBAM.bam input, outputs of GATK's generated CRAM match CRAMTools generated CRAM, but not samtools/PrintReads SAM output, as things like insert sizes are different.
If required for other tools, CRAM indexes must be generated via CRAMTools until we can generate them via CRAMFileWriter.

Generation of exampleCRAM.cram:
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram
* java -jar cramtools-2.1.jar index -I public/gatk-utils/src/test/resources/exampleCRAM.cram --bam-style-index

CRAM generation by existing tools:
* samtools view -C -T public/gatk-utils/src/test/resources/exampleFASTA.fasta -o testSamtools.cram public/gatk-utils/src/test/resources/exampleBAM.bam
* java -jar cramtools-2.1.jar cram --ignore-md5-mismatch --capture-all-tags -Q -n -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -O testCRAMTools.cram
* java -jar target/executable/GenomeAnalysisTK.jar -T PrintReads -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleBAM.bam -o testGATK.cram

CRAMTools view of the above:
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I public/gatk-utils/src/test/resources/exampleCRAM.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testSamtools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testCRAMTools.cram | tail -n 1
* java -jar cramtools-2.1.jar bam --skip-md5-check -R public/gatk-utils/src/test/resources/exampleFASTA.fasta -I testGATK.cram | tail -n 1
 		2015-01-26 14:47:39 -03:00
licensing Updated license information 2014-10-14 17:10:12 -04:00
protected Added introductory CRAM support. 2015-01-26 14:47:39 -03:00
public Added introductory CRAM support. 2015-01-26 14:47:39 -03:00
settings/helpTemplates Output JSON version of docs for Galaxy 2014-10-09 06:42:25 -04:00
.gitignore Fixed bug using GraphBased due to infinite likelihoods resulting from the calculation of alignment cost of very long insertion or deletions (done in linear scale) 2014-04-01 16:14:52 -04:00
README.md Update README file for the 2.6 release 2013-06-20 13:08:29 -04:00
ant-bridge.sh Added faster built executable, non-packaged jars. 2014-11-05 00:30:46 +08:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
pom.xml Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00

README.md

The Genome Analysis Toolkit

See http://www.broadinstitute.org/gatk/