known-sites for Felis_catus_9.0 (GCA_000181335.4)
Answered
Good afternoon dear members,
I am running gatk BaseRecalibrator and one of the required parameters is --known-sites - One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.
Does anyone know where I can find a VCF file similar to those in GATK resources bundle available for humans?
Thank you
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Hi Vladimir Makarov, this is a great question! Unfortunately, we as the GATK developers don't have any resources for feline DNA. It might be worth asking in forums like https://www.biostars.org/ or other places where people might have resources on feline DNA. If you are successful with your search feel free to post an update here if you want, this helps other users who come across this post in the future.
Thank you for your understanding,
Michael -
>> Unfortunately, we as the GATK developers don't have any resources for feline DNA.
Dear Michael,
Two weeks ago I have downloaded 14 aligned WGS BAM files sequenced at Broad Institute. Sequences were aligned at Broad institute using standard GATK pipeline. gatk BaseRecalibrator is one of the steps and --known-sites is required parameter. Therefore, this resource exists. I was wondering if it can be shared. Thank you very much,
Vlad
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Hi Vladimir Makarov,
It is very possible that some groups at the Broad are doing feline research and have generated this resource for themselves. However, we as the developers of GATK don't distribute them as part of our best practices workflows. Do you know which group processed these 14 samples? They might be able to point you to that resource.
Best,
Michael -
I just got a hint from Biostars, in case someone else asks:
https://ftp.ensembl.org/pub/release-109/variation/vcf/felis_catus/
Thank you
Vlad
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