picard | command line tools | Genomics library
kandi X-RAY | picard Summary
kandi X-RAY | picard Summary
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.
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Top functions reviewed by kandi - BETA
- 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
picard Key Features
picard Examples and Code Snippets
Community Discussions
Trending Discussions on picard
QUESTION
I have the following Azure AD service principal in my terraform module.
...ANSWER
Answered 2022-Mar-11 at 00:31You 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:
QUESTION
I can't seem to get GATK to recognise the number of available threads. I am running GATK (4.2.4.1) 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
:
ANSWER
Answered 2022-Feb-15 at 17:02In 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:
QUESTION
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?
...ANSWER
Answered 2021-Sep-22 at 17:08Yes, 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:
QUESTION
When I load from memory everything works fine
...ANSWER
Answered 2021-Sep-06 at 10:55You have to add autoLoad the store or load it manually.
QUESTION
I would like to transform my nested json message and take only required filed using Jolt spec-
My Input JSON :
...ANSWER
Answered 2021-Jul-17 at 19:18Tip : 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
QUESTION
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:
...ANSWER
Answered 2021-Jul-03 at 16:38From 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:
QUESTION
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.
...{38-keys,fit-out,closed,eddy-tamy,datechange-feb2025,staff-onboard,sandy-brighton,open-dec2020}
{same-year,budgeted,signature-done,mark-picard,hotel,5-keys}
{active,building,itsa-signed,2322-keys,pending-signature,next-year-(construction),opening-feb2024}
ANSWER
Answered 2021-Apr-01 at 09:27- 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).
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
):
QUESTION
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:
...ANSWER
Answered 2021-Apr-04 at 18:34You should just swap the two if
statements where you make a recursive call, so that you first visit rightReport
and then later leftReport
.
QUESTION
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:
...ANSWER
Answered 2021-Apr-03 at 07:22findOfficersWithNoDirectReports() {
// 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;
}
QUESTION
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
...ANSWER
Answered 2021-Mar-06 at 17:13You can use protocols:
Create protocol with given fields, and make all DataType1,2 etc classes conform to it:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install picard
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 .
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