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1. Ran bwa index -a bwtsw GCF_002127325.2_HanXRQr2.0-SUNRISE_genomic.fna.gz by hand in an interactive node

2. Commands are in 0_assem.nf. Run this with nextflow run -bg 0_assem.nf -c teton.config. These are jobs are using: module load swset/2018.05 gcc/7.3.0 bwa/0.7.17 samtools/1.12 as specified in teton.config in this directory (bwa is version 0.7.17-r1188). Output is in /project/microbiome/data/seq/HMAX1/assem/sambam/. Gave each job 60 minutes, which was unnecessarily long, but conservative. Longest running jobs I could see were less than 20 minutes. Moved all 477 inputs files through in about 30 minutes total. There are 476 sorted bam files (according to ls sambam/*sorted.bam | wc -l).

Variant calling

• 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.

• variants/0_Completed this step with something like: sbatch --account=evolgen --time=0-02:00 --nodes=1 --mem=120G --mail-type=END  0_call_variants.sh is running

Copying steps from https://github.com/zgompert/DimensionsExperiment

• Variant filtering with vcfFilter.pl and filterSomeMore.pl

Started notes in 1_filter_variants.sh

• Variant filtering

Used the following filters: 2X coverage (2302 reads), 10 alt. reads, not fixed, Man-Whitney P for BQB = 0.01, Man-Whitney P for RPB = 0.01, minimum mapping quality 30, missing data for fewer than 230 (80% with data), biallelic SNPs only.

Ended up with 64,061 SNPs in /uufs/chpc.utah.edu/common/home/gompert-group2/data/dimension_lyc_gbs/Variants/filtered2x_lmel_variants.vcf.

Next, I dropped SNPs with > mean + 3 SD coverage (possible repeats). This left 63,194 SNPs in morefilter_filtered2x_lmel_variants.vcf.

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