WHITEHALL MARKETING GROUPBusiness Directories,Company Directories

Company Name: Corporate Name:	WHITEHALL MARKETING GROUP
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Company Address:	1800 Hunicke St,EDWARDSVILLE,IL,USA
ZIP Code: Postal Code:	62025-1049
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Fax Number:	6186568400 (+1-618-656-8400)
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USA SIC Code(Standard Industrial Classification Code):	874214
USA SIC Description:	Marketing Consultants
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Picard Tools - By Broad Institute
Use Picard Tools The tools, which are all listed further below, are invoked as follows: java jvm-args -jar picard jar PicardToolName OPTION1=value1 OPTION2=value2 See the Tool Documentation for details on the Picard command syntax and standard options as well as a complete list of tools with usage recommendations, options, and example commands
Tool documentation - Broad Institute
Be sure to consult the Frequently Asked Questions (FAQ) page for useful information about typical problems you may encounter while using Picard tools
Picard Metrics Definitions - Broad Institute
Picard A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM BAM CRAM and VCF View the Project on GitHub broadinstitute picard Latest Jar Release; Source Code ZIP File; Source Code TAR Ball; View On GitHub; Picard Metrics Definitions
Frequently Asked Questions - Broad Institute
A: Most Picard tools can do this To read from stdin, specify dev stdin as the input file To write to stdout, specify dev stdout as the output file, and also add the option QUIET=true to suppress other messages that otherwise would be written to stdout
SAM Differences in Picard - Broad Institute
A number of Picard tools can handle secondary alignments, but typically these tools either ignore these alignments or pass them from input to output unchanged MergeBamAlignment has the PRIMARY_ALIGNMENT_STRATEGY that can be used to determine how the program will select a primary alignment among multiple alignments for a segment in an aligner's
InsertSizeMetrics (PICARD JDK API Documentation) - Broad Institute
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension " insert_size_metrics"
AddOrReplaceReadGroups (PICARD JDK API Documentation) - Broad Institute
Do the work after command line has been parsed RuntimeException may be thrown by this method, and are reported appropriately
CollectInsertSizeMetrics (PICARD JDK API Documentation) - Broad Institute
Field Detail Histogram_R_SCRIPT protected static final java lang String Histogram_R_SCRIPT See Also: Constant Field Values; Histogram_FILE @Option(shortName="H", doc="File to write insert size Histogram chart to ") public java io File Histogram_FILE; DEVIATIONS
HsMetrics (PICARD JDK API Documentation) - Broad Institute
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets
DownsampleSam (picard 2. 10. 9-1-gaa8c979-SNAPSHOT API) - Broad Institute
Class to randomly downsample a BAM file while respecting that we should either retain or discard all of the reads for a template - i e all reads with the same name, whether first or second of pair, secondary or supplementary, all travel together