different line length in sequence
Error using samtools mpileup
[fai_load] build FASTA index.
[fai_build_core] different line length in sequence 'REFERENCE'.
The lines in the reference sequence fasta-file does not have all the same length.
(1) Edit manually
Convert the reference sequence into a single line by removing all newlines "\n".
(2) Picard tool
# use Picard to normalize the reference fasta file