Hi all, I used GenomicsDBImport to generate a genomic database from a bunch of gvcf files corresponding to a number of genomic intervals. For each interval, GenomicsDBImport produced a directory with contents that look like this:
[rmarcondes@boslogin02 db_180]$ pwd
/n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_180
[rmarcondes@boslogin02 db_180]$ ls -a
. 111$1$5060538 114$1$7908999 117$1$5787846 callset.json vidmap.json
.. 112$1$3923849 115$1$2315063 118$1$2797076 __tiledb_workspace.tdb
110$1$3996139 113$1$1360579 116$1$1734749 119$1$4990981 vcfheader.vcf
Now I want to use Gathervcfs to merge all my gvcfs into a single vcf file. I assumed the files I needed to put through Gathervcfs were the "vcfheader.vcf" file in each interval directory, like this:
java -Xmx200g -XX:ParallelGCThreads=20 -jar $GATKPATH GatherVcfs \
-I /n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_3/vcfheader.vcf \
-I /n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_4/vcfheader.vcf \
-I /n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_5/vcfheader.vcf \
-I /n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_227/vcfheader.vcf \
-I /n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_228/vcfheader.vcf \
-I /n/holyscratch01/edwards_lab/rafa/genomic_DBs/db_229/vcfheader.vcf \
-O thevcf.vcf
But that just produced an empty vcf file with no variants, just a header and a list of all contigs.
What gives? Thanks for any pointers!
1 answer
The first thing that comes to mind when I see this is that the vcfheader.vcf, as aptly named, probably only contain VCF headers. This would make sense given that GenomicsDBImport is supposed to create a genomics DB workspace from a VCF file.
In other words, you're combining header files and expecting data to be populated out of thin air.
See this: https://github.com/Intel-HLS/GenomicsDB/wiki/Importing-VCF-data-into-GenomicsDB
Your data is probably in one of the JSON files.
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Error in GATK GenomicsDBImport
written by raf.marcondes •