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• Following steps from https://github.com/zgompert/DimensionsExperiment.

• Built bcftools version 1.16 and installed in /project/evolgen/bin/.

• bcftools needed 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=8G --mail-type=END  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

  Filtered vcf with 1_filter_variants.sh, which contains notes on the criteria that I used (could be altered to suit).

To do:

• Summarize the parse report files in /gscratch with some code to iterate over all the individual reports and get an overall count.