Samtools mpileup : error reading from input file

Question

I am writing a code to analyse yeast sequencing data using R. I was able to do the alignment using BWA and thus obtain a .bam file and its .bai index using samtools. My next step is to perform variant calling using bcftools. Here is my command line and the associated error:

vcf_file <- "pathway/to/stock/variants.vcf"
system(paste("samtools mpileup -f", paste(fasta_dir, "chr*.fa", sep = ""), merged_bam_file,
              "| bcftools call --ploidy 1 -mv >", vcf_file))

[mpileup] 17 samples in 17 input files samtools mpileup: error reading from input file Failed to read from standard input: unknown file type

• paste(fasta_dir, "chr*.fa", sep = "") gives the pathway to the directory containing the 17 fasta files of the genome of reference (one for each chromosome), named chrI.fa, chrII.fa, ...

• merged_bam_file is pathway to the alignment file I obtained and with which I want to perform the variant calling

I understand that the problem comes from the type of my files, but since the alignment file is BAM and my genome of reference is FASTA, I have absolutely no clue what to change to make it work. Any advices?

Thank you for your help :)