21-BCFtools_Bowtie2.sh

#!/bin/bash

# This program calls variants in BAM files generated by Bowtie2 and sorted and indexed by samtools using bcftools

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# Specifying input and output path variables that are consistent over the loop #
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PATH_IN_BAMS=/media/rna/INIA/benchmark/Alignment/Bowtie2/Alignment_BAM
PATH_REF_FILE=/media/rna/INIA/benchmark/Alignment/Bowtie2/Reference_Bowtie2/DM_1-3_516_R44_potato_genome_assembly.v6.1.fa
PATH_VCF_OUT=/media/rna/INIA/benchmark/Variant_calling/BCF_Tools/Bowtie2/VCF_output
mkdir -p $PATH_VCF_OUT
PATH_STAT_OUT=/media/rna/INIA/benchmark/Variant_calling/BCF_Tools/Bowtie2/stat
mkdir -p $PATH_STAT_OUT

# Calculating number of total input samples
TOTAL_SAMPLES=$(ls -l $PATH_IN_BAMS | grep -c ^d)

for folder in ${PATH_IN_BAMS}/*; do
	sample=$(basename $folder)

    # Output path and name for the VCF file for every sample
    VCF_OUT_FILE=$PATH_VCF_OUT/${sample}.vcf
    # Specifying file name for compuation times for every sample
    COMP=${PATH_STAT_OUT}/computation_times_${sample}.txt
    #reads= samtools view -c $PATH_IN_BAMS/$sample/*_sorted*.bam

    bcf_start=`date +%s`
    bcftools mpileup -f  $PATH_REF_FILE $PATH_IN_BAMS/$sample/*_sorted*.bam -d 250 | bcftools call --ploidy 2 -mv -o $VCF_OUT_FILE
    bcf_end=`date +%s`
    bcf_time=$(($bcf_end-$bcf_start))
    echo "bcftools variant calling time in s ($sample):	$bcf_time" >> $COMP

done