If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: (Docker image) (GATK) v126.96.36.199-32-g1e4a397-SNAPSHOT
b) Exact command used: (MANY VARIATIONS of the following, although this works to create a folder per contig):
while read in;
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 \
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?
|||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 ):
Unless you can recommend an alternative way of generating the invariant sites?
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