I have a directory of .fasta files and .fasta.fai files. I am trying to use those as a reference sequence to the samtools mpileup command for reads in a different directory (BAM-Format):
for i in * do ../../../../../../samtools-1.2/samtools mpileup ../Sorted_bam/Sorted_Aligned_$i.bam.bam -f $i -d 16847 -g -P flat > $i.bcf done
But when I run it I get the error:
[mpileup] 1 samples in 1 input files [fai_load] build FASTA index. [fai_load] fail to open FASTA index.
14 times (there are 14 files). What am I be doing wrong?
Thanks in advance.