#!/bin/bash
FILE_PATH="data/trimmed_fastq_small/"
find "$FILE_PATH" -name "*.fasta" |
while IFS= read -r my_file
do
filename=$(basename "$my_file")
basename=$(basename "$my_file" .fasta)
echo $basename
mkdir -p results/sam results/bam results/bcf results/vcf
bwa mem trimmed_fastq_small/$filename > results/sam/$basename.aligned.sam
samtools view -S -b results/sam/$basename.aligned.sam > results/bam/$basename.aligned.bam
samtools sort -o results/bam/$basename.sorted.bam results/bam/$basename.aligned.bam
bcftools mpileup -O b -o results/bcf/$basename.bcf -f data/ref_genome/sequences.fasta results/bam/$basename.sorted.bam
bcftools call --ploidy 1 -m -v -o results/bcf/$basename.vcf results/bcf/$basename.bcf
vcfutils.pl varFilter results/bcf/$basename.vcf > results/vcf/$basename.vcf
bgzip -c results/bcf/$basename.vcf > results/bcf/$basename.vcf.gz
tabix -p vcf results/bcf/$basename.vcf.gz
done
mkdir "Variant_Results"
cp -r results/bcf/*.vcf Variant_Results/
rem mkdir "Variant_Results_of_COVID_gz"
rem cp -r results/bcf/*.vcf.gz Variant_Results_of_COVID_gz/
rem cp -r results/bcf/*.vcf.gz.tbi Variant_Results_of_COVID_gz/
bcftools merge results/bcf/*.vcf.gz -Oz -o Merge_Final_Variants.vcf.gz
gunzip Merge_Final_Variants.vcf.gz
