# Ungzip, bgzip, and create an index file.
for CHR in 01 02 03 04 05 06 07 08 09 10 11 12 13 14; do
sbatch -J Pf3D7_${CHR}_v3.pf.clean_vcf -N 1 -n 1 -t 1-0 --mem=2G -p batch --account=ccmb-condo -o logs/Pf3D7_${CHR}_v3.pf.clean_vcf-%A.out -e logs/Pf3D7_${CHR}_v3.pf.clean_vcf-%A.err --mail-type=FAIL [email protected] --wrap="module load tabix; gunzip -d ./vcf_data/init_vcfs/Pf3D7_${CHR}_v3.pf7.vcf.gz; bgzip ./vcf_data/init_vcfs/Pf3D7_${CHR}_v3.pf7.vcf; tabix -p vcf ./vcf_data/init_vcfs/Pf3D7_${CHR}_v3.pf7.vcf.gz"
done

# Create new records for SNV variants at multiallelic sites.
for CHR in 01 02 03 04 05 06 07 08 09 10 11 12 13 14; do
sbatch -J Pf3D7_${CHR}_v3.pf.split_records -N 1 -n 1 -t 1-0 --mem=100G -p batch --account=ccmb-condo -o logs/Pf3D7_${CHR}_v3.pf.split_records-%A.out -e logs/Pf3D7_${CHR}_v3.pf.split_records-%A.err --mail-type=FAIL [email protected] --wrap="module load bcftools; bcftools norm -m -snps -Oz -o ./vcf_data/init_vcfs/Pf3D7_${CHR}_v3.pf7.split_records.vcf.gz ./vcf_data/init_vcfs/Pf3D7_${CHR}_v3.pf7.vcf.gz"
done

# Example usage.
for CHR in 01 02 03 04 05 06 07 08 09 10 11 12 13 14; do
sbatch -J Pf3D7_${CHR}_v3.pf.identify_dups -N 1 -n 1 -t 1-0 --mem=2G -p batch --account=ccmb-condo -o logs/Pf3D7_${CHR}_v3.pf.identify_dups-%A.out -e logs/Pf3D7_${CHR}_v3.pf.identify_dups-%A.err --mail-type=FAIL [email protected] --wrap="module load tabix python; python ./ppg/vcfs/identify_duplicate_records.py Pf3D7_${CHR}_v3.pf7 Pf3D7_${CHR}_v3 /users/dpeede/data/dpeede/13_plasmodium/vcf_data/init_vcfs /users/dpeede/data/dpeede/13_plasmodium/vcf_data/dup_info | bgzip > /users/dpeede/data/dpeede/13_plasmodium/vcf_data/dup_info/Pf3D7_${CHR}_v3.pf7.dup_records.vcf.gz"
done