Download by clicking the "Download R for (Mac) OS X" link to the wget https://github.com/broadinstitute/picard/releases/download/2.20.1/picard.jar To call the GATK .jar file directly this works as a command after installing JAVA8 as noted
Where is your jarfile and where are you trying to do that? And what's your classpath? 10 Oct 2019 I copied the jar file to the google bucket associated with the which I'm also setting as an input variable `picard_jar` to `gs://bucket/picard.jar`. You can download a zipped package containing the jar file from the Latest Release project page on Github. The file name will be of the format picard-tools-x.y.z.zip. CRAM format specification and java API for read data. - enasequence/cramtools Tools for using Picard and GATK with the Google Genomics API. - googlegenomics/gatk-tools-java snpEff with HGVS annotations for nucleotide changes ***NOT THE Official snpEff Repository*** - DBHi-BiC/snpEff
Suite of tools for processing BRB-seq data. Contribute to DeplanckeLab/BRB-seqTools development by creating an account on GitHub. A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. - broadinstitute/picard Contribute to WhiteLab/Dnaseqse development by creating an account on GitHub. gatk-tools-java$ mkdir ../picard/lib/gatk-tools-java gatk-tools-java$ cp target/gatk-tools-java*minimized.jar ../picard/lib/gatk-tools-java/ No other words and lines are allowed. /path/to/programs /path/to/inputfile /path/to/outputfile thread_number ex1: /home/user_name /media/user_name/disk1/input /home/user_name/output 8 ex2: ~ ~/input ~/output 8 2. So for example, a simple Picard command would look like: It downloads the Cromwell JAR file automatically to a temporary location; a compatible java JRE must be available. You can use the -r/--jar option if you already have a local copy of Cromwell; other Cromwell configuration options are…
CRAM format specification and java API for read data. - enasequence/cramtools Tools for using Picard and GATK with the Google Genomics API. - googlegenomics/gatk-tools-java snpEff with HGVS annotations for nucleotide changes ***NOT THE Official snpEff Repository*** - DBHi-BiC/snpEff Suite of tools for processing BRB-seq data. Contribute to DeplanckeLab/BRB-seqTools development by creating an account on GitHub. A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. - broadinstitute/picard Contribute to WhiteLab/Dnaseqse development by creating an account on GitHub.
Contribute to lmoncla/illumina_pipeline development by creating an account on GitHub. VAP : For Reference mapping and Variant detection. - modupeore/VAP Tribble codec for JSON. Contribute to lindenb/jsontribble development by creating an account on GitHub. Tool for converting Blastn query results to the SAM format - AstrorEnales/BlastToSam Contribute to databio/rnapipe development by creating an account on GitHub. Make a ribosomal RNA interval_list for Picard Tools CollectRnaSeqMetrics - hg19.rRNA.interval_list
Scripts for reproducing results from neoepiscope paper - pdxgx/neoepiscope-paper
