valgartner/DRC_vivax

Genomic insights into Plasmodium vivax population structure and diversity in central Africa This repository contains code and steps used for investigating *Plasmodium vivax* evolutionary history in central Africa using whole genome sequencing data. This work is now published in Malaria Journal: doi.org # *P. vivax* Sample Data All samples used in this study can be found in the metadata table: `sample_info/metadata_table.csv`. Multiplicity of Infection (MOI) was determined using the following steps: 1. generate two vcfs: one polyclone with a max of 3 clones, and one a gvcf which indicates the level of coverage at each base. The commands to generate these are in `make-fastas-6.sh` ``` $ octopus -I ${DEDUP_BAM} -R ${REF} -T LT635626 -o api.poly3.vcf.gz --annotations AD -C polyclone --max-clones 3 --threads 16 --sequence-error-model PCR $ octopus -I ${DEDUP_BAM} -R ${REF} -T LT635626 -o api.g.vcf.gz --annotations AD --refcall POSITIONAL --threads 16 --sequence-error-model PCR ``` 2. `check-accessions.py` scans the genomes2 directory that contains directories/files like ERR12355/api.poly3.vcf.gz . It produced the simple text file genomes2/mono-0.9.txt with lines like ``` ERR773745 OK ERR773746 PolyClonal ERR773747 NoGVCF ERR773748 OK ``` The 0.9 indicates that a site is considered homozygous if the major allele frequency is 0.9. Run it like `check-accesions.py --cutoff 0.9 --allowed-het-sites=1 > mono-0.9.txt` Create the list of accessions with `grep OK mono-0.9.txt | cut -f1 > mono-0.9-accs.txt` Accessions with no MOI data were included by default. # Variant Calling All scripts needed to download, map to PvP01 reference genome, and do variant calling are included in the `genome_processing` directory. ## Download fastq and map to PvP01 reference genome Run `get-haploid-gvcf.sh` using the command ``` $ sbatch get-haploid-gvcf.sh accessions.txt ``` where "accessions.txt" contains one run accession number per line. This script will launch individual bash scripts via an array for each accession numbe …