I am trying to find an open source vcf of known variants for Anopheles gambiae s.s, which I can use for filtering with GATK VQSR (GATK Variant Filtration), instead of using hard filtering. Is this available anywhere?
I am also looking for this Anopheles gambiae P4 file: gs://vo_agam_production/resources/observatory/ag.allsites.nonN.vcf.gz which is referenced in the SNP genotyping pipeline https://github.com/malariagen/pipelines/blob/v0.0.4/docs/specs/snp-genotyping-vector.md. I'm not able to download this directly.
I'd be very grateful for some help! Thank you!
I have searched and have been unable to find these files. I tried downloading from gs and was denied.