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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/

19 questions
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Unrecognized option: I picard.jar

I am trying to convert a BMA file into FASTQ format, using picard.jar. This is my command: java -jar /opt/picard-tools/picard.jar SamToFastq \ I=chr2chr3.bam \ FASTQ=chr2chr3.f1.fastq \ SECOND_END_FASTQ=chr2chr3.f2.fastq However I got this error…
Hamid_UMB
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How to deal with trailing garbage caused from unzipping the hs37d5 fastq file

I have really tried to sort this problem out but it seems like no one else faced this problem before. I unzipped the fastq file from the 1000G: gunzip -c **hs37d5.fa.gz** | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}'…
M.Phillips
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Picard SamToFastq only extracts one read, then throws an error

I'm trying to extract some FastQ files from bam files. Picard can do this with SamToFastq as it says in the documentation for this tool it accepts either a bam or sam file. But when I run it, it only extracts one read, and then exits. Here is the…
Davy Kavanagh
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Unable to access jar file (installed in a conda virtual environment)

I've tried to execute a few different commands in picard (currently AddOrReplaceReadGroups; see below), but get the error: "Unable to access jarfile". I've tried all of the solutions to this seemingly common problem but can't seem to resolve this.…
Quinn
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