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Questions tagged [picard]

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files.

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files.

See https://broadinstitute.github.io/picard/

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VCF4.2 file not recognised by GATK

Ive seen a lot having the same problem, but I havnt found a solution yet. I have supplied 24 VCF4.1 files (http://evs.gs.washington.edu/EVS/) to GATKs CombineVariants. I get this error: ##### ERROR MESSAGE: Invalid command line: No tribble type was…
user2966591
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Is there a way to set parameters for the Java VM when using a Snakemake wrapper?

When using tools like picard or fgbio through snakemake wrappers, I keep running into out-of-memory issues. At the moment I resort to direct shell calls, which allow me to set the VMs memory. I would prefer to pass these parameters to the wrapped…
Krischan
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An interesting cron, bash, perl and java problem

Essentially, I have a perl workflow that runs a suite of java tools via the system command (picard in GATK4 for those of you who are familiar with Broad Institute's software). These gatk4 commands return code 0 if successful. When I kick off the…
sirisha sunkara
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R How to obtain the coefficients of a polynomial expression?

Hi and thank you for your time, I realize my question is in fact very similar to the question in this thread: How to get coefficients of polynomial expression However, I would like to elaborate on this question. I have written a program which when…
Anon
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How does one set the RAM and CPU parameters for java programs running in an anaconda environment?

In a standard Linux environment with java installed, I can run the any java program using the command: java -jar path/to/picard.jar Where picard is an example of a java program. I can also specify how many CPU threads or RAM the JVM should use…
Glubbdrubb
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How to get consensus sequence from BAM file format on java (by means of Picard)

How can I view the Picard BAM file format using Java?
user1437708
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Reorganize music library with Picard or another program

I want to rename/reorganize my music library for easy reading off a LCD screen, on my CDJs and on my car stereo this is the goal, this is not a functional script. my script attempt is doing it: %albumartist% || VA - %albumname% / %tracknumber%…
austin
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picard estimated_library_size too high

I have a question regarding the picard markduplicates tool. I almost always get very high numbers in the estimated_library_size field (160-190 million) that is nothing like expected library size or the number of reads I get from the sequencing…
StlCh
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Why is Picard MarkDuplicates deleting .bam files in place of .bai files in my Snakemake workflow?

I have done some looking but I cant figure out why picard markduplicates is deleting my bam files and replacing with bai files? I am wanting the metrics and bam files. I am also wanting the bai files and then rename this file to .bam.bai for…
Genetics
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Why doesn't subprocess.Popen() give live feed?

I'm working on an automated framework for a bioinformatics tool. As most software that my program will use is written for Linux and not written in python, I use subprocess to invoke the processes. The problem I have is that many steps in the…
biomedswe
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MarkDuplicates Picard

I am using Picard to mark only optical duplicates for which I read the manual of MarkDuplicates. My script looks like this #!/usr/bin/bash java -jar build/libs/picard.jar MarkDuplicates \ I=sorted.bam \ O=mark_opticalduplicate.bam \ …
Bandana
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How to convert fastq to uBAM with picard dock on google cloud

I have been trying to convert my fastq files on google cloud to uBAM files but no success so far. Here is code I used: dsub \ --project projectID \ --zones "us-central1-*" \ --logging gs://bucket/logging \ --image broadinstitute/picard \ --command…
Bingley
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linux merge multiple files in picard

I have ten directories, and each directory has around 10-12 bam files. I need to use picard package to merge them together and I want to find a way to do it better. basic command: java -jar picard.jar MergeSamFiles \ I=input_1.bam \ …
Peter Chung
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Picard SortSam speed up?

I'm wondering how to speed up picard's SortSam? It takes a long time to run it and I know GATK can be multi-threaded but I have not found example on Picard yet. I'm wondering how other people tackle this problem?
jackyen_2000
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Does picard markduplicate toggle PCR duplicate samflag

I have a RNA-seq bam file and there are few reads that are puzzling me. According to the bam header, this bam file is sorted by coordinate, created using tophat and markduplicate step is not done. But some reads are marked for being duplicate in the…
svural
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