Hello, I am doing SNP calling, using the pipeline as follows: 1. index the reference fasta file using bwa. 2. align the read file using bwa aln command. 3. converted the .sai file to .sam file. 4. converted .sam to the .bam file using samtools. 5.constructed mpileup file using samtools. 6.called SNP in the form of .vcf file using bcftools.
but as a result, i m getting empty vcf file.and during the process, there is no error shown by the tools I have used. what may be the reason for this I m not getting. please help.