Picard 2.20.7 freeware

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

Author Sourceforge
Released 2019-09-16
Filesize 15.7001953125 MB
Downloads 862
OS Windows XP, Windows Vista, Windows Vista x64, Windows 7, Windows 7 x64, Windows 8, Windows 8 x64, Windows 10, Windows 10 x64
Installation Instal And Uninstall
Keywords Sequence Alignment Map, bioinformatics tool, BAM manipulation, sequence, bioinformatics, manipulate
Users' rating
(9 rating)
Picard - Freeware Download Notice

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Picard freeware - The Latest User Reviews
Picard freeware - The Latest Versions History
2.20.7 Sep 16, 2019 New Release Initial Move Calculate the detail metric correctly (on a per-genotype basis). Add more tests Add test to handle multi-sample VCF Refactor detail->summary metrics accumulation. Fix CreateVerifyIDIntensityContaminationMetricsFile to handle LLK and LLK0 as doubles. Added new metric, refined naming of others. Enhanced multiple sample tests.
Updating gradle to 5.6 (#1380)
Updating NIO dependency and fixing a dependency issue (#1391)
Update to htsjdk 2.20.3 (#1381)
Extend travis build matrix to separate Barclay tests from legacy tests. (#952)
PO-18867 Catch NaN Percent_Duplication edge case (#1389)
1.119 Sep 2, 2014 New Release Updated AbstractOpticalDuplicateFinder to handle post-CASAVA 1.8 read names. Pass READ_NAME_REGEX=null to skip optical duplicate detection in MarkDuplicates.
Fixed RevertSam to harmonize different quality score encoding schemes when the sanitize option is set.
Modified Casava18ReadNameEncoder to correctly display filter status.
SamPairUtil: Added the ability to set the mate cigar tag on supplementary alignments. Updated AbstractAlignmentMerger to set mate cigars when merging supplementary alignments.
CollectWgsMetrics: Added 2 new metrics- the fraction of bases attaining 15X and 25X coverage respectively.
Added a new tool, CollectBaseDistributionByCycle, that computes the nucleotide distribution per cycle.
FileAppendStreamLRUCache: Added wrapping of FileOutputStreams with BufferedOutputStreams.
Fixed a bug in BCF2Writer where it was double-closing the output stream.
Fixed VariantContext to ignore symbolic alleles when running strict validation for a VCF.
1.118 Aug 4, 2014 New Release Fixed index out of bounds exception in CollectTargetedPcrMetrics.
Get IntelDeflater working again -- had been disabled since package name change.
Genotype.java: Add a function to determine if a genotype is heterozygous non-reference (e.g. C/T if the reference is A)
HardyWeinbergCalculation.java: Fixed HW statistic overflow at large sample numbers.
Update TribbleIndexedFeatureReader.java, TabixReader.java, and TabixFeatureReader.java to add new constructor with given index file. Update AbstractFeatureReader.java to pass index file forward to specific readers. Pass index file in AbstractFeatureReader to underlying readers.
Fixed race condition where synchronouslyClose() would be called multiple times if AbstractAsyncWriter.close() called twice simultaneously. Allowing close() to be called multiple times as per java.io.Closeable interface specifications.
FastqReader: added constructor, toString, removed extra-line.

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