https://bioinformaticsonline.com/snippets/view/43108/corona-variant-calling-steps? https://bioinformaticsonline.com/snippets/view/43108/corona-variant-calling-steps Fri, 25 Jun 2021 09:57:05 -0500 https://bioinformaticsonline.com/snippets/view/43108/corona-variant-calling-steps #!/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]]> Rahul Nayak