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Badly formed genome unclippedLoc: Query interval "20" is not valid for this input.

Hay, I tried using GenomicsDBImport with 28 samples. I tried to load my data using a sample map file (tab separated sample header and their absolute paths) but on using the command -

gatk --java-options "-Xmx40g -Xms2g" GenomicsDBImport --genomicsdb-workspace-path /mnt/drive/Exome_data/PROCESSING/gatk4_processing/genome_db/demo_DB  --batch-size 25 -L 20  --sample-name-map sample.map --tmp-dir=/mnt/exome/tmp --reader-threads 40

I actually want to load all the variants, not just small intervals of them. Using -L 20 gives me the error in the header.

My questions are two-fold -
1) I take it that -L 20 effectively means chr20, then why am I getting the following error?
2) If I create a DB importing only from chr20, can I add the same samples to the same DB, but with different intervals, so that I can import all the chromosomes? Or would I need to keep separate DB for each chromosome?

I've tried my best to understand, but I think I'm surely missing something!

Any help appreciated.

Answers

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