GenomicsDBImport -L [string] (but for the whole genome): purpose to generate invariant sites
Answered
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: (Docker image) (GATK) v4.0.2.1-32-g1e4a397-SNAPSHOT
b) Exact command used: (MANY VARIATIONS of the following, although this works to create a folder per contig):
while read in;
do
gatk --java-options "-Xmx40g" GenomicsDBImport --reader-threads 30 -V ../F2014_female_fall_DrosEU_match.g.vcf.gz \
-V ../MR19female2.g.vcf.gz -V ../MR20female1.g.vcf.gz -V ../MR20male2.g.vcf.gz -V \
../F2015_female_fall_DrosEU_match.g.vcf.gz -V ../MR19male1.g.vcf.gz -V ../MR20female2.g.vcf.gz -V \
../MR_female.g.vcf.gz -V ../MR19female1.g.vcf.gz -V ../MR19male2.g.vcf.gz -V ../MR20male1.g.vcf.gz -V \
../MR_male.g.vcf.gz --genomicsdb-workspace-path allsamples_$in \
--L "$in";
done < intervals.list
c) Entire error log: If I give it a bed file, which i have seen on the forums, or multiple -L commands
A USER ERROR has occurred: More than one interval specified. The tool takes only one
If not an error, choose a category for your question(REQUIRED):
a)How do I (......)?
Please could you tell me how to pass the -L argument more than one contig?
|
--intervals -L |
[] | One or more genomic intervals over which to operate |
In the docs, pasted above it states that one or more (more is required here) interval can be posted. I would like to create the GenomicsDBImport for the whole genome (and some other projects may have many hundreds of contigs)
Can you create one single GenomicsDBImport database for the whole genome
WHY am I ding this: I have create g.vcf.gz for all the sample. To analyse them with pixy (https://pixy.readthedocs.io/en/latest/) I require invariant sites to be created in the output. They recommend this approach (GenomicsDBImport ):
https://pixy.readthedocs.io/en/latest/generating_invar/generating_invar.html
Unless you can recommend an alternative way of generating the invariant sites?
regards,
Peter Thorpe
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Hi Pete Thorpe,
GenomicsDBImport can take more than one interval. I noticed that you are using a very old version of GATK: 4.0.2.1. We are currently on 4.2.4.1 and there have been major changes to GenomicsDBImport, so this problem you are having could be an old bug.
Could you try with a newer version of GATK?
Best,
Genevieve
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Thank you for your reply. I downloaded the docker images on: Nov 19 2021 (15:44) - something strange must have happened here.
I have just downloaded the new image and this is the version: gatk-package-4.2.4.1-local.jar
I will try this.
Thank you, Pete
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VERSION FIX:
My download command (which pulled down an old version): singularity pull docker:docker broadinstitute/gatk
what did pull down the correct version (Redhat 6.9, running on centos 7):
singularity pull docker:broadinstitute/gatk:latest
Now trying on Rocky Linux 8. This worked:
singularity pull docker://broadinstitute/gatk
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I tried this with a bed file:
gatk --java-options "-Xmx40g" GenomicsDBImport --reader-threads 20 -V ../F2014_female_fall_DrosEU_match.g.vcf.gz \
-V ../MR19female2.g.vcf.gz -V ../MR20female1.g.vcf.gz -V ../MR20male2.g.vcf.gz -V \
../F2015_female_fall_DrosEU_match.g.vcf.gz -V ../MR19male1.g.vcf.gz -V ../MR20female2.g.vcf.gz -V \
../MR_female.g.vcf.gz -V ../MR19female1.g.vcf.gz -V ../MR19male2.g.vcf.gz -V ../MR20male1.g.vcf.gz -V \
../MR_male.g.vcf.gz --genomicsdb-workspace-path allsamples -L ../dmel-all-chromosome-r6.43.bedA USER ERROR has occurred: More than one interval specified. The tool takes only one
can you please give me an example of how -L can take multiple options? (Also add this to the docs?)
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The docker image version now says: v4.0.2.1-32-g1e4a397-SNAPSHOT ... I just downloaded this.
Is dockerhub upto date?
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Yes, the docker hub is up to date. Maybe there is an issue for which gatk version you have in your path.
I start my docker image this way and it has always worked for me:
docker run -it broadinstitute/gatk:4.2.4.1
Here is an article we have regarding running GATK with Docker: https://gatk.broadinstitute.org/hc/en-us/articles/360035889991--How-to-Run-GATK-in-a-Docker-container
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Thank you for your time. I have add a "version fix" to a comment above. Lesson learn for me just assuming it pulled down the latest. (sorry).
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Oh good I'm glad to hear that you have it working now! Thanks for writing in so we could get GATK working for you!
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