consensus.sh

#!/bin/bash

echo Generating consensus sequences

export PATH=$PATH:/home/username/bowtie2-2.1.0:/home/username/samtools:/home/username/samtools/bcftools:/home/username/samtools/misc

roots=(
SN7640178_10172_8183
SN7640178_10173_8265
SN7640178_10174_8266
SN7640178_10175_8267
)

for x in ${roots[@]}; do
        echo Piling up ${x}
  samtools mpileup -uf reference_SGD/S288C_reference_genome_R64-1-1_20110203/S288C_reference_sequence_R64-1-1_20110203.fsa alignments/"$x"_sorted.bam.bam | bcftools view -cg - | vcfutils.pl vcf2fq > pileups/"$x"_cons.fq&
done