samtools mpileup -uf REFERENCE.fasta SAMPLE_sorted.bam [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 java -jar picard.jar NormalizeFasta I=REFERENCE.fasta O=normalized_REFERENCE.fasta |
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