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Following steps from https://github.com/zgompert/DimensionsExperiment.
Built bcftools version 1.16 and installed in
/project/evolgen/bin/.bcftoolsneeded reference genome in bzip2 format, not gzip. So I now simply have an unzipped reference genome, which I have reindexed.Completed this step with something like:
sbatch --account=evolgen --time=1-00:00 --nodes=1 --mem=120G 8G --mail-type=ENDÂ 0_call_variants.sh(this took 12 hours and 40 minutes and 552 MB of RAM; I asked for 120GB, which likely gave me the whole node and made it a bit faster)Filtering vcf:
Started notes in
1_filter_variants.sh
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