Hi,

I need to convert vcf to fasta and after make multifasta file. However I am stuck in getting empty output files with this script

I would like to ask for a help

#!bin/bash
for file in $inpath/*.filtered ;
do
        echo $file
        bname=$(basename $file)
        echo "base name is $bname"
        bfile=$outpath1/$bname".gz"
        outfile=$outpath/$bname".fasta"
        bgzip -c $file > $bfile
        bcftools index $bfile
        samtools faidx $reference | bcftools consensus -s $bfile -o $outfile
done