I'm curious as to why MarkDuplicatesWithMateCigar has the "This tool cannot be used with alignments that have large gaps or reference skips, which happens frequently in RNA-seq data." limitation?
Thanks Louis On 14-10-08 11:25 AM, George Grant wrote: > Picard Release 1.122 > 8 October 2014 > > - New Command Line Program "GenotypeConcordance" > -- Calculates the concordance between genotype data for two samples in > two different VCFs - one being considered the truth (or reference) the other > being considered the call. The concordance is broken into separate results > sections for SNPs and indels. Summary and detailed statistics are reported. > Note that for any pair of variants to compare, only the alleles for the > samples under interrogation are considered and MNP, Symbolic, and Mixed > classes of variants are not included. > > - New Command Line Program "UpdateVcfDictionary" > -- Updates the sequence dictionary of a VCF from another file (SAM, BAM, > VCF, dictionary, interval_list, fasta, etc). > > - New Command Line Program "VcfToIntervalList" > -- Create an interval list from a VCF > > - New Command Line Program "MarkDuplicatesWithMateCigar" > -- A new tool with which to mark duplicates: > This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR > (MC) optional tags > pre-computed (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and > FixMateInformation). This allows the new tool to perform a streaming > duplicate > marking routine (i.e. a single-pass). This tool cannot be used with > alignments that have large gaps or reference skips, which happens > frequently in RNA-seq data. > > There were many refactors of the old MarkDuplicates and > MarkDuplicatesWithMateCigar, since the share common code. > EstimateLibraryComplexity was caught up in this too. > > Many, many, many unit tests were added to were added to prove > equivalency of MarkDuplicatesWithMateCigar to MarkDuplicates. This also > exposed a few one in a million corner cases in MarkDuplicates both in > duplicate marking as well as optical duplicate detection. This results > in MarkDuplicates needing to write slightly larger temporary files when > running. SamFileTester was also improved to handle the various test > cases for duplicate marking testing. > > - Updates to IntervalList: > -- Added capacity to create a simple interval list from a string (the > name of the contig) > -- Added the capacity to subtract one interval list from another > (currently > it would only work if they were both wrapped inside a container) > > - Updates to SamLocusIterator > -- Performance optimizations gaining about 35% speed up... > > - Updates to MarkDuplicates: > -- Removed unnecessary storage of a string in the Read Ends in Mark > -- Clarifed the size of ReadEndsForMarkDuplicates > > - Updated the minimum number of times that the BAIT_INTERVALS (in > CalculateHsMetrics) and TARGET_INTERVALS (in CollectTargetedMetrics) must be > set to one. > > - Moved CollectHiSeqPfFailMetrics into picard public > > - Updates to documentation generation (internal): > -- changed link to IntervalList.java documentation > -- updated how _includes/command-line-usage.html is generated > > - Moved SAMSequenceDictionaryExtractor and tests from picard to htsjdk > > - George > > > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > > > > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
