zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public
History
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
..
VectorPairHMM Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml 2015-01-06 10:32:11 -05:00
c After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. 2014-05-19 17:36:41 -04:00
chainFiles The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
doc Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Added introductory CRAM support. 2015-01-26 14:47:39 -03:00
gatk-engine Added introductory CRAM support. 2015-01-26 14:47:39 -03:00
gatk-queue Faster builds, with updates to documentation generation. 2014-11-05 00:32:23 +08:00
gatk-queue-extensions-generator Split all imports of tools|engine from utils, and all tools from engine. 2014-10-24 20:59:46 +08:00
gatk-queue-extensions-public Adding Axiom_Exome_Plus.sites_only.all_populations.poly.vcf to the resource bundle because it is used in the v3.3 best practices 2015-01-05 14:52:31 -05:00
gatk-root Bumping HTSJDK version to pickup a bug fix for CRAM. 2015-01-26 14:47:39 -03:00
gatk-tools-public Added -trimAlternates argument to SelectVariants 2015-01-21 21:33:35 -05:00
gatk-utils Added introductory CRAM support. 2015-01-26 14:47:39 -03:00
gsalib Updated gsalib version to 2.1 for resubmitting with updated license to CRAN 2014-12-09 17:07:48 -05:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Split all imports of tools|engine from utils, and all tools from engine. 2014-10-24 20:59:46 +08:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Bumping HTSJDK version to pickup a bug fix for CRAM. 2015-01-26 14:47:39 -03:00
src/main Added faster built executable, non-packaged jars. 2014-11-05 00:30:46 +08:00
pom.xml Update pom versions to mark the start of GATK 3.4 development 2014-10-23 22:31:44 -04:00