picard | command line tools | Genomics library

 by   broadinstitute Java Version: 3.0.0 License: MIT

kandi X-RAY | picard Summary

kandi X-RAY | picard Summary

picard is a Java library typically used in Artificial Intelligence, Genomics applications. picard has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has high support. You can download it from GitHub, Maven.

For user questions please look for answers and ask first in the GATK forum. A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats. Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF. Picard now builds and passes tests under Java 11. This should be considered to be a Beta feature. As of version 2.0.1 (Nov. 2015) Picard requires Java 1.8 (jdk8u66). The last version to support Java 1.7 was release 1.141. Running legacyTest uses the legacy commandline parser while barclayTest uses the new parser.

            kandi-support Support

              picard has a highly active ecosystem.
              It has 873 star(s) with 354 fork(s). There are 166 watchers for this library.
              There were 1 major release(s) in the last 12 months.
              There are 231 open issues and 530 have been closed. On average issues are closed in 103 days. There are 20 open pull requests and 0 closed requests.
              It has a negative sentiment in the developer community.
              The latest version of picard is 3.0.0

            kandi-Quality Quality

              picard has 0 bugs and 0 code smells.

            kandi-Security Security

              picard has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              picard code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              picard is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              picard releases are available to install and integrate.
              Deployable package is available in Maven.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              It has 86115 lines of code, 5270 functions and 721 files.
              It has medium code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed picard and discovered the below as its top functions. This is intended to give you an instant insight into picard implemented functionality, and help decide if they suit your requirements.
            • Performs the actual analysis
            • Create a map of query intervals for a VCF file
            • Calculates the edit distance between two strings
            • The difference between two alleids
            • Initialize the reference genome
            • Lift a VariantContext to a specific interval
            • Left aligns a sequence to an existing variant
            • Swap the ref and alt and alt fields of a VariantContext
            • Performs the actual processing
            • Accumulate triples
            • Check the validity of the lane
            • Do the actual work
            • Computes the detailed statistics for the jumping library
            • Compute the distance between the input and the linecode
            • Generate indexes
            • Reads the input file and writes it to the output file
            • Load up the target file
            • Read the header from the input file
            • Creates and dumps the files
            • Performs the actual work
            • Combines multiple SAM files
            • Reads the code files and creates them
            • Performs the Picard work
            • Load the sequence files
            • Export all the required metrics
            • Main method to process the input BAM file
            Get all kandi verified functions for this library.

            picard Key Features

            No Key Features are available at this moment for picard.

            picard Examples and Code Snippets

            No Code Snippets are available at this moment for picard.

            Community Discussions


            Terraform for loop in a for loop
            Asked 2022-Mar-11 at 00:32

            I have the following Azure AD service principal in my terraform module.



            Answered 2022-Mar-11 at 00:31

            You have to re-organize your app_role_assignments and then flatten it. If you want principal_object_id to have more then one value, it should always be a list, even for a single element:

            Source https://stackoverflow.com/questions/71425779


            GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread
            Asked 2022-Feb-15 at 17:02

            I can't seem to get GATK to recognise the number of available threads. I am running GATK ( in a conda environment which is part of a nextflow (v20.10.0) pipeline I'm writing. For whatever reason, I cannot get GATK to see there is more than one thread. I've tried different node types, increasing and decreasing the number of cpus available, providing java arguments such as -XX:ActiveProcessorCount=16, using taskset, but it always just detects 1.

            Here is the command from the .command.sh:



            Answered 2022-Feb-15 at 17:02

            In case anyone else has the same problem, it turned out I had to configure the submission as an MPI job.

            So on the HPC I use, here is the nextflow process:

            Source https://stackoverflow.com/questions/71053941


            How to get a custom MP3 tag via Python?
            Asked 2021-Oct-04 at 18:34

            I am working on an algorithm that uses AcousticBrainz API. Part of the process is assigning an audio file with a specific UUID that refers to a file in a database. The tag is added via Picard and is present among other tags when checking e.g. via VLC Media Player:

            Is there any way to access these 'custom' tags? I tried to use eyeD3 and mutagen, however, I think they only enable accessing specific tags like artist or length of the file.

            Can I use eyed3 or mutagen to accomplish the goal? Is there any other tool that enables such operation?



            Answered 2021-Sep-22 at 17:08

            Yes, you can use either one. These custom tags are stored as user text frames, with the frame ID "TXXX".

            Here's some example code with eyeD3:

            Source https://stackoverflow.com/questions/69287671


            Ext.grid.Panel loading from other domain
            Asked 2021-Sep-06 at 10:55

            When I load from memory everything works fine



            Answered 2021-Sep-06 at 10:55

            You have to add autoLoad the store or load it manually.

            Source https://stackoverflow.com/questions/69056802


            JSON to JSOn jolt transformation
            Asked 2021-Jul-18 at 18:46

            I would like to transform my nested json message and take only required filed using Jolt spec-

            My Input JSON :



            Answered 2021-Jul-17 at 19:18

            Tip : Looking at outer part of the results array by using "*": "&" while looking at the inner part of that, and combining them under name key which seems to be unique as a grouping by criteria for the desired result set such as

            Source https://stackoverflow.com/questions/68422911


            Force a certain rule to execute at the end
            Asked 2021-Jul-13 at 19:12

            My question is very similar to this one.

            I am writing a snakemake pipeline, and it does a lot pre- and post-alignment quality control. At the end of the pipeline, I run multiQC on those QC results.

            Basically, the workflow is: preprocessing -> fastqc -> alignment -> post-alignment QCs such as picard, qualimap, and preseq -> peak calling -> motif analysis -> multiQC.

            MultiQC should generate a report on all those outputs as long as multiQC support them.

            One way to force multiqc to run at the very end is to include all the output files from the above rules in the input directive of multiqc rule, as below:



            Answered 2021-Jul-03 at 16:38

            From your comments I gather that what you really want to do is run a flexibly configured number of QC methods and then summarise them in the end. The summary should only run, once all the QC methods you want to run have completed.

            Rather than forcing the MultiQC rule to be executed in the end, manually, you can set up the MultiQC rule in such a way that it automatically gets executed in the end - by requiring the QC method's output as input.

            Your goal of flexibly configuring which QC rules to run can be easily achieved by passing the names of the QC rules through a config file, or even easier as a command line argument.

            Here is a minimal working example for you to extend:

            Source https://stackoverflow.com/questions/68118582


            How to extract a number marked with specific word from text string in Google Data Studio
            Asked 2021-May-05 at 14:13

            I have a text string that contains several instances of numbers, example of the data is below.

            I am trying to extract the number of keys (the number that is followed by the text -keys). I tried several REGEXP_EXTRACT patterns without luck.






            Answered 2021-Apr-01 at 09:27
            0) Summary
            • Use #1 OR #2 OR #3 below (added two additional suggestions as the author received an error with #1 and then #2 in regards to the CAST function which may be a result of spacing, Data Source (PostgreSQL) specific or another issue).
            1) With CAST

            It can be achieved by using the Calculated Field below (where Field represents the respective field name) which extracts all digits immediately preceding -keys; the CAST function was added to ensure that the field Type is Number (the default field Type of REGEXP_EXTRACT values are Text); also, for future reference, the Raw Input Literal R was used so that \d represents the sequence for a digit vs the default (without R) in Google Data Studio, which requires two back slashes (\\d):

            Source https://stackoverflow.com/questions/66899431


            How do I sort a Binary Search Tree from greatest to least?
            Asked 2021-Apr-04 at 19:24

            I need to return an array of nodes sorted from high to low. At the moment I am trying to implement an inorder traversal which gives me the exact opposite of what I'm looking for.

            The tree looks like:



            Answered 2021-Apr-04 at 18:34

            You should just swap the two if statements where you make a recursive call, so that you first visit rightReport and then later leftReport.

            Source https://stackoverflow.com/questions/66944539


            How do I stop a Binary Search Tree Traversal?
            Asked 2021-Apr-03 at 07:22

            I need to traverse a binary search tree and return an array of the leaf nodes. At the moment I am traversing through the entire tree and returning one node at a time.

            My tree looks like:



            Answered 2021-Apr-03 at 07:22
            findOfficersWithNoDirectReports() {
                // If this is a leaf node, return the officer name
                if (!this.leftReport && !this.rightReport) {
                  return [this.officerName]
                // Otherwise, combine the left and right results 
                val result = []
                if (this.leftReport) {
                  result = result.concat(this.leftReport.findOfficersWithNoDirectReports());
                if (this.rightReport) {
                  result = result.concat(this.rightReport.findOfficersWithNoDirectReports());
                return result;

            Source https://stackoverflow.com/questions/66925947


            Swift function that can return various types
            Asked 2021-Mar-06 at 17:35

            Is it possible for a function to return a specific Data Type based on the parameter entered?

            Here's an example of what I'm trying to do:

            I've defined different datatypes that will hold data from an API call



            Answered 2021-Mar-06 at 17:13

            You can use protocols:

            Create protocol with given fields, and make all DataType1,2 etc classes conform to it:

            Source https://stackoverflow.com/questions/66508294

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install picard

            You can download it from GitHub, Maven.
            You can use picard like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the picard component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .


            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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