Heads up:
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.
Notice:
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.
Attention:
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!

Syntax problem with VariantRecalibrator

jphekmanjphekman Broad InstituteMember

Running VariantRecalibrator on GATK 4.1.0.0. (I know it's an older version - I need this version due to issues in more recent versions with functionality at a different step in my pipeline from this one. Also, I have tested this step on 4.1.2.0 and get the same error.)

My command line:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx10G -jar /seq/vgb/software/gatk/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar VariantRecalibrator -R /seq/references/Canis_lupus_familiaris_assembly3/v1/Canis_lupus_familiaris_assembly3.fasta -V /seq/vgb/jphekman/singleBamToVcf/31001701034247.vcf --resource dbsnp,known=true,training=false,truth=false,prior=2.0:/seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an InbreedingCoeff -mode SNP -O /seq/vgb/jphekman/singleBamToVcf/31001701034247.recal --tranches-file /seq/vgb/jphekman/singleBamToVcf/31001701034247.tranches --rscript-file /seq/vgb/jphekman/singleBamToVcf/31001701034247.plots.R

The error:

A USER ERROR has occurred: Couldn't read file file:///home/unix/jphekman/dbsnp,known=true,training=false,truth=false,prior=2.0:/seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz. Error was: It doesn't exist.

Note that both /seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz and /seq/vgb/references/dog/population_variation/dog_dbSNP.vcf.gz.tbi do exist.

I've seen this error previously when I was using incorrect syntax in the --resources parameter. However I have perused the doc and I can't see where I'm going wrong. (Apologies if I'm missing something obvious.)

https://software.broadinstitute.org/gatk/documentation/tooldocs/4.1.0.0/org_broadinstitute_hellbender_tools_walkers_vqsr_VariantRecalibrator.php

Help - what am I missing?

Best,
Jessica

Best Answers

Answers

Sign In or Register to comment.