gatk | Official code repository for GATK versions | Genomics library

by broadgsa Java Version: 3.8-1 License: No License

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | gatk Summary

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

The Genome Analysis Toolkit.

Support

Quality

Security

License

Reuse

Support

gatk has a low active ecosystem.

It has 289 star(s) with 226 fork(s). There are 68 watchers for this library.

It had no major release in the last 12 months.

gatk has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of gatk is 3.8-1

Quality

gatk has 0 bugs and 0 code smells.

Security

gatk has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

gatk code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

gatk does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

gatk releases are available to install and integrate.

Build file is available. You can build the component from source.

gatk saves you 102451 person hours of effort in developing the same functionality from scratch.

It has 110345 lines of code, 10173 functions and 1137 files.

It has medium code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed gatk and discovered the below as its top functions. This is intended to give you an instant insight into gatk implemented functionality, and help decide if they suit your requirements.

Called after a traversal has been completed
Calculates the NRD value for the nucleotide counts
Calculates the number of occurrences in the hypothesis counts
Calculates the OC coordinate counts for the nucleotide counts
Decodes and returns a SampileupFeature
Parses bases and qualifiers
Parse the indels
Entry point to the BWT
Reads a BWT from the input stream
synthetic tests
Updates the reference context
Returns an iterator over the file pointers
Generate a table report for each read group
Generate an annotated reference context
Computes the mean and variance
Initializes the statistics
Initialize aminoAcids
Performs a batch alignment
Initialize the VCF writer
Create a new BWT files from the given reference sequence
This is called when a read is required
Find the index of the event for an event context
The main benchmark
Main execution method
Populate the events for the nucleotide
Read a VCF element from a file

Get all kandi verified functions for this library.

gatk Key Features

No Key Features are available at this moment for gatk.

gatk Examples and Code Snippets

No Code Snippets are available at this moment for gatk.

Community Discussions

Trending Discussions on gatk

Add flag -I before multiple input in snakemake

Create as many files as the number of items from two lists with the same number of items in Python

Create a command on crontab that stream editor and rewrite a file every 15 minutes

awk script to cut/paste a string in a file

create a generator that substitutes a pattern in a file

Apply across rows in dbplyr (postgresql). Getting "Error: Unknown input type: pairlist"

Snakemake 200000 job submission

Parse a file of strings in python separated by newline into a json array

Create index of a reference genome with bwa and gatk using snakemake touch

Bootstrap4 - center span and inside link vertically

QUESTION

Add flag -I before multiple input in snakemake

Asked 2021-Jun-02 at 08:13

I am using snakemake to describe the GATK pipeline. I need to run the following command:

...

ANSWER

Answered 2021-Jun-02 at 08:13

You could do this:

Source https://stackoverflow.com/questions/67799734

QUESTION

Create as many files as the number of items from two lists with the same number of items in Python

Asked 2021-Mar-08 at 11:32

Consider the file testbam.txt:

...

ANSWER

Answered 2021-Mar-08 at 11:32

First, and even if it is unrelated to the question, some of your code is not really Pythonic:

Source https://stackoverflow.com/questions/66528299

QUESTION

Create a command on crontab that stream editor and rewrite a file every 15 minutes

Asked 2021-Feb-18 at 07:08

Let's say I have a file with patterns to match into another file:

file_names.txt

...

ANSWER

Answered 2021-Jan-25 at 11:46

It might be easier to create a daemon/background process as opposed to a periodic cron job.

Source https://stackoverflow.com/questions/65881231

QUESTION

awk script to cut/paste a string in a file

Asked 2021-Feb-11 at 18:37

i got a file formatted like that : (each space = tab separator)

...

ANSWER

Answered 2021-Feb-08 at 11:01

With your shown samples, could you please try following. Written and tested in GNU awk.

Source https://stackoverflow.com/questions/66066371

QUESTION

create a generator that substitutes a pattern in a file

Asked 2021-Jan-25 at 06:56

Please consider the following list:

...

ANSWER

Answered 2021-Jan-25 at 06:56

Two functions, for readability. You can surely combine them into one single one.

Source https://stackoverflow.com/questions/65879803

QUESTION

Apply across rows in dbplyr (postgresql). Getting "Error: Unknown input type: pairlist"

Asked 2021-Jan-15 at 08:47

I'm trying to filter on a condition that at least one of three columns has a value other than "".

My code works on a data.frame (or tibble), but on a raw DBI table I get an error:

Error: Unknown input type: pairlist

...

ANSWER

Answered 2021-Jan-15 at 08:47

Turns out only #3 (from below) works on DBI tables.

Source https://stackoverflow.com/questions/65732502

QUESTION

Snakemake 200000 job submission

Asked 2020-Nov-18 at 14:53

I have 200000 fasta sequences. I am doing GATK to call variants and created a wildcard for every sequence. Now I would like to submit 200000 jobs using snakemake. Will this cause a problem to cluster? Is there a way to submit jobs in a set of 10-20?

...

ANSWER

Answered 2020-Nov-18 at 14:53

First off, it might take some time to calculate the DAG, but I have been told the DAG calculation recently has been greatly improved. Anyways, it might be wise to split up in batches.

Most clusters won't allow you to submit more than X jobs at the same time, usually in the range of 100-1000. I believe the documentation is not fully correct, but when using --cluster cluster I believe the --jobs argument controls the number of active/submitted jobs at the same time, so by using snakemake --jobs 20 --cluster "myclustercommand" you should be able to control this. Know that this control the number of submitted jobs, not active jobs. It might be that all your jobs are in the queue, so probably best to check in with your cluster administrator and ask what the maximum number of submitted jobs is, and get as close to that number.

Source https://stackoverflow.com/questions/64892007

QUESTION

Parse a file of strings in python separated by newline into a json array

Asked 2020-Nov-12 at 10:11

I have a file called path_text.txt its contents are the 2 strings separated by newline:

...

ANSWER

Answered 2020-Nov-12 at 09:15

see below

Source https://stackoverflow.com/questions/64800939

QUESTION

Create index of a reference genome with bwa and gatk using snakemake touch

Asked 2020-Oct-26 at 10:27

I align reads with bwa and call variants with gatk. gatk needs the creation of a dict for the reference genome, and bwa needs creation of indices. When I use touch for both of them I get this error:

...

ANSWER

Answered 2020-Oct-23 at 12:27

Why don't you simply define the dict file as an input of the gatk rule and the ìndex as an input of the bwa rule?

Source https://stackoverflow.com/questions/64499458

QUESTION

Bootstrap4 - center span and inside link vertically

Asked 2020-Oct-15 at 13:11

I have 7 button links inside table, I added icons by using span and make them bigger I used "class=bigger", but now I am struggling with centering span and the rest of the text vertically (and horizontally) inside button.

...

ANSWER

Answered 2020-Oct-15 at 11:59

I tried your code and it works fine, the span and icon are centered horizontally and vertically.

Is it possible that you have a margin-top or padding-top somewhere on your links?

Source https://stackoverflow.com/questions/64368710

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

Vulnerabilities

No vulnerabilities reported

Install gatk

You can download it from GitHub.
You can use gatk 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 gatk 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 .

Support

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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