Step 4: Variant Calling (bcftools mpileup call) - rsalani13/EPP622-2026-SNPCalling GitHub Wiki

Commands

cd ../
mkdir variant_calling_4
cd variant_calling_4/

ln -s ../bwamem2_3/*bam* .

#somewhere along the line i accidentally moved my references into my bwamem folder...
#so that’s where we are gonna call the symbolic reference files from
ln -s ../bwamem2_3/sacCer3.fa*

#make bam list
ls *bam > bam_list.txt

nano variant_calling.sh
-----------------------------------------------------------------
bcftools mpileup \
  -Ou \
  -q 5 \
  -b bam_list.txt \
  -f /lustre/isaac24/proj/UTK0505/rsalani/exam2/analyses/variant_calling_4/sacCer3.fa \
  -a AD,ADF,ADR,DP,SP | \
bcftools call \
  -m \
  -v \
  -Oz \
  -o variant_script_output.raw.vcf.gz

bcftools stats  variant_script_output.raw.vcf.gz > variant_output.raw.stats.txt
bcftools filter -i 'TYPE="snp" & INFO/MQ>=40 & FORMAT/DP>=10' -o variant_filtered.vcf.gz variant_script_output.raw.vcf.gz
bcftools stats variant_filtered.vcf.gz > variant_filtered.stats.txt
done
-----------------------------------------------------------------

bash variant_calling.sh

Results

bcftools stats report path and name: /lustre/isaac24/proj/UTK0505/rsalani/exam2/analyses/variant_calling_4/variant_filtered.stats.txt