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GenomicsDBimport - correct syntax several intervals/chromosomes

I read this blog-post from Geraldine "UsingGenomicsDBImport in practice";
https://gatkforums.broadinstitute.org/gatk/discussion/11813/how-to-consolidate-gvcfs-for-joint-calling-with-genotypegvcfs
saying something about how to import several chromosomes;

gatk GenomicsDBImport \
-V data/gvcfs/mother.g.vcf \
-V data/gvcfs/father.g.vcf \
-V data/gvcfs/son.g.vcf \
--genomicsdb-workspace-path my_database \
--intervals chr20,chr21

So I used similar With
-L 1, 2 (like above)

When I do similar with my gvcfs (there are no "Chr" in the chromosome-names) I get an error mesage;
"A USER ERROR has occurred: Badly formed genome unclippedLoc: Query interval "1,2" is not valid for this input."
When I use -L 1 the program runs and I can continue successfully With GenotypeGVCFs
When I use -L 1 -L 2 the program runs, but there (seems to be) no data for chromosome 2 (and maybe more errors too)?

Q1:
what is the correct syntax if I want to make batches of several chromosomes?
Q2:
In this blog-post ( https://gatkforums.broadinstitute.org/gatk/discussion/24371/a-problem-about-genomicsdbimport-and-combinegvcfs#latest ) it is said (bhanuGandham ) that; "GenomicsDBImport is used for samples in the order of thousands. For <1000 samples it is better to use CombineGVCFs". This was New information.
Is 1000 an "official/recommended" limit for the number of WGS-samples to GenomicsDBImport resp CombineGVCFs?
Is a sample an individual with all chromosomes or is it meant one interval/chromosome from 1000 individuals?

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    1. what is the correct syntax if I want to make batches of several chromosomes?

    Please review the following doc on ways to provide intervals to gatk article#4133, and confirm you are using the right format as mentioned in this post

    1. Is 1000 an "official/recommended" limit for the number of WGS-samples to GenomicsDBImport resp CombineGVCFs?

    Yes, please read the caveat section of the CombineGVCFs tool docs

    1. Is a sample an individual with all chromosomes or is it meant one interval/chromosome from 1000 individuals?

    The former, please review the GATK Best Practices Data Preprocessing and Germline short variant discovery

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