Tool documentation. Adds comments to the header of a BAM file. This tool makes a copy of the input bam file, with a modified header that includes the comments specified at the command line prefixed by CO. Use double quotes to wrap comments that include whitespace or special characters. Note that this tool cannot be run on SAM files. Java Data Structures 2nd Edition End of the World Production, LLC. Free Statistical Software This page contains links to free software packages that you can download and install on your computer for standalone offline, nonInternet. Java Program To Calculate Mean Median Mode' title='Java Program To Calculate Mean Median Mode' />Usage example java jar picard. Add. Comments. To. Bam Iinput. bam Omodifiedbam. Ccomment1 Ccomment 2Option. Description. INPUT FileInput BAM file to add a comment to the header Required. OUTPUT FileOutput BAM file to write results Required. Durufle Prelude Fugue Alain Pdf Download. COMMENT StringComments to add to the BAM file Default value null. This option may be specified 0 or more times. Add. Or. Replace. Read. Groups. Replace read groups in a BAM file. This tool enables the user to replace all read groups in the INPUT file with a single new read group and assign all reads to this read group in the OUTPUT BAM file. For more information about read groups, see the GATK Dictionary entry. This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health GA4. GH see http ga. Usage example java jar picard. Add. Or. Replace. Read. Groups Iinput. Ooutput. bam RGID4 RGLBlib. Java Program To Calculate Mean Median Mode' title='Java Program To Calculate Mean Median Mode' />Overview of SQL for Analysis and Reporting. Oracle has enhanced SQLs analytical processing capabilities by introducing a new family of analytic SQL functions. IEEE Projects Trichy, Best IEEE Project Centre Chennai, Final Year Projects in Trichy We Provide IEEE projects 2017 2018, IEEE 2017 Java Projects for M. EM. Tech. Algorithm. A series of repeatable steps for carrying out a certain type of task with data. As with data structures, people studying computer science learn about. Vol. 7, No. 3, May, 2004. Mathematical and Natural Sciences. Study on Bilinear Scheme and Application to Threedimensional Convective Equation Itaru Hataue and Yosuke. Smu assignments, smu mba assignments, smu mba summer solved assignments, smu mba summer assignments sem 1, smu mba sem 1 assignments, smu mba sem 1 solved assignments. MS Paint, the first app you used for editing images, will probably be killed off in future updates of Windows 10, replaced by the new app Paint 3D. Microsoft lists. RGPLillumina RGPUunit. RGSM2. 0Option. Description. INPUT StringInput file BAM or SAM or a GA4. GH url. Required. OUTPUT FileOutput file BAM or SAM. Required. SORTORDER Sort. OrderOptional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. Default value null. Possible values unsorted, queryname, coordinate, duplicate, unknown RGID StringRead Group ID Default value 1. This option can be set to null to clear the default value. RGLB StringRead Group library Required. RGPL StringRead Group platform e. Required. RGPU StringRead Group platform unit eg. Required. RGSM StringRead Group sample name Required. RGCN StringRead Group sequencing center name Default value null. RGDS StringRead Group description Default value null. International Journal of Environmental Research and Public Health, an international, peerreviewed Open Access journal. RGDT Iso. 86. 01. DateRead Group run date Default value null. RGPI IntegerRead Group predicted insert size Default value null. RGPG StringRead Group program group Default value null. RGPM StringRead Group platform model Default value null. Bait. Designer. Designs oligonucleotide baits for hybrid selection reactions. This tool is used to design custom bait sets for hybrid selection experiments. The following files are input into Bait. Designer a TARGET interval list indicating the sequences of interest, e. DESIGNNAME. The tool will output intervallist files of both bait and target sequences as well as the actual bait sequences in Fast. A format. At least two baits are output for each target sequence, with greater numbers for larger intervals. Although the default values for both bait size 1. Offsets represent the distance between sequential baits on a contiguous stretch of target DNA sequence. The tool will also output a pooled set of 5. This redundancy achieves a uniform concentration of oligonucleotides for synthesis by a vendor as well as equal numbersof each bait to prevent bias during the hybrid selection reaction. Usage example java jar picard. Bait. Designer TARGETtargets. DESIGNNAMEnewbaits Rreferencesequence. Option. Description. TARGETS FileThe file with design parameters and targets Required. DESIGNNAME StringThe name of the bait design Required. REFERENCESEQUENCE FileThe reference sequence fasta file Required. LEFTPRIMER StringThe left amplification primer to prepend to all baits for synthesis Default value ATCGCACCAGCGTGT. This option can be set to null to clear the default value. RIGHTPRIMER StringThe right amplification primer to prepend to all baits for synthesis Default value CACTGCGGCTCCTCA. This option can be set to null to clear the default value. DESIGNSTRATEGY Design. StrategyThe design strategy to use to layout baits across each target Default value Fixed. Offset. This option can be set to null to clear the default value. Possible values Centered. Constrained, Fixed. Offset, Simple BAITSIZE IntegerThe length of each individual bait to design Default value 1. This option can be set to null to clear the default value. MINIMUMBAITSPERTARGET IntegerThe minimum number of baits to design per target. Default value 2. This option can be set to null to clear the default value. BAITOFFSET IntegerThe desired offset between the start of one bait and the start of another bait for the same target. Default value 8. This option can be set to null to clear the default value. PADDING IntegerPad the input targets by this amount when designing baits. Padding is applied on both sides in this amount. Default value 0. This option can be set to null to clear the default value. REPEATTOLERANCE IntegerBaits that have more than REPEATTOLERANCE soft or hard masked bases will not be allowed Default value 5. This option can be set to null to clear the default value. POOLSIZE IntegerThe size of pools or arrays for synthesis. If no pool files are desired, can be set to 0. Default value 5. This option can be set to null to clear the default value. FILLPOOLS BooleanIf true, fill up the pools with alternating fwd and rc copies of all baits. Equal copies of all baits will always be maintained Default value true. This option can be set to null to clear the default value. Possible values true, false DESIGNONTARGETSTRAND BooleanIf true design baits on the strand of the target feature, if false always design on the strand of the genome. Default value false. This option can be set to null to clear the default value. Possible values true, false MERGENEARBYTARGETS BooleanIf true merge targets that are close enough that designing against a merged target would be more efficient. Default value true. This option can be set to null to clear the default value. Possible values true, false OUTPUTAGILENTFILES BooleanIf true also output. Default value true. This option can be set to null to clear the default value. Possible values true, false OUTPUTDIRECTORY FileThe output directory. If not provided then the DESIGNNAME will be used as the output directory Default value null. Bam. To. Bfq. Create BFQ files from a BAM file for use by the maq aligner. BFQ is a binary version of the FASTQ file format. This tool creates bfq files from a BAM file for use by the maq aligner. Usage example java jar picard. Bam. To. Bfq Iinput. ANALYSISDIRanalysisdir OUTPUTFILEPREFIXoutputfile1 PAIREDRUNfalse. Option. Description. INPUT FileThe BAM file to parse. Required. ANALYSISDIR FileThe analysis directory for the binary output file. Required. FLOWCELLBARCODE StringFlowcell barcode e. PYMAAXX. Required. Cannot be used in conjuction with options OUTPUTFILEPREFIXLANE IntegerLane number. Default value null. Cannot be used in conjuction with options OUTPUTFILEPREFIXOUTPUTFILEPREFIX StringPrefix for all output files Required. Cannot be used in conjuction with options FLOWCELLBARCODE F LANE LREADSTOALIGN IntegerNumber of reads to align null all. Default value null. READCHUNKSIZE IntegerNumber of reads to break into individual groups for alignment Default value 2. This option can be set to null to clear the default value. PAIREDRUN BooleanWhether this is a paired end run. Required. Possible values true, false RUNBARCODE StringDeprecated option use READNAMEPREFIX instead Default value null.