>From a bam file I'd like to extract the alignment, for each aligning read, corresponding to the 10 bp region contig1:100-109 of the read, writing it as fasta. This would produce something like
>1/1 ACGTACGTAC >20/1 ACGTAC-TAC >22/1 C-GTACG-AC . . . It seemed a combo of "samtools view ... contig1:100-109" and "samtools fasta" would do the trick but I haven't had luck with it yet. Any suggestions?
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