We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Picard in Docker
Dear GATK/Picard team,
I am new to Picard and was just about to build it, when I noticed that there is a Picard Docker image available - great idea! Is this functional yet? I couldn't find any instructions on how to use it. I gave it a try and did the following:
pulled the picard image
docker pull broadinstitute/picard
then I am trying to run it like so:
docker run -i -t broadinstitute/picard FastqToSam -h
This gives me the usage for FastqToSam so I thought I was on the right track.
However, when running a full fetched command like:
sudo docker run -i -t broadinstitute/picard FastqToSam F1=009_S1_L001_R1_001.fastq.gz F2=009_S1_L001_R2_001.fastq.gz O=test.bam SM=female
I get the following error:
[Tue Aug 25 20:09:49 UTC 2015] picard.sam.FastqToSam FASTQ=009_S1_L001_R1_001.fastq.gz FASTQ2=F1=009_S1_L001_R2_001.fastq.gz OUTPUT=test.bam SAMPLE_NAME=female USE_SEQUENTIAL_FASTQS=false READ_GROUP_NAME=A SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 25 20:09:49 UTC 2015] Executing as [email protected] on Linux 3.13.0-54-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14; Picard version: 1.138() JdkDeflater
[Tue Aug 25 20:09:49 UTC 2015] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Cannot read non-existent file: /usr/picard/009_S1_L001_R1_001.fastq.gz
It seems as if Picard in the container can't find my input files. How would I pass my files correctly to the container?
Any help would be much appreciated!!
Thanks in advance for your time!