mpileup error

[alyamahmoud]

Hi All

I am trying to use mpileup for SNP calling.

I have illumina reads which I aligned to reference using bwa, sorted the bam files, indexed the referencer and ran samtools mpileup as follows:

samtools mpileup -uf ref.fa sample1.sorted.bam> k1.mpileup

I then try to bcftools as follows:
bcftools view -bvcg k1.mpileup

first I get that option -b is invalid, when I remove it and just run the command as is without -b: I get the error below.

[vcf.c:643 bcf_hdr_read] invalid BCF2 magic string: only BCFv2.2 is supported.
Failed to open or the file not indexed: k1.bcf

I am really stuck, can anyone help ?

I am using samtools version 1.19
thanks a lot
Alyaa