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Make mpileup file with several BAM files

Have you tried using samtools mpileup in.bam [in2.bam [...]]? Here's information about the output format from the manual page: The first three columns give the ...
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2 votes

need bam file for pilon

Run a short-read mapper. For example: bwa index assembled.fasta bwa mem -pt16 assembled.fasta read1.fq.gz read2.fq.gz \ | samtools sort -m4G -@4 -o align.bam -
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