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obtain reference and base from read in a region from a bam file

Hi

I want to obtain the reference base and the base of the reads that align in a certain region from a bam file. And get something like this:

      Reference           Read1             Read2
          A                 A           indel or mismatch
          C                 G                  C
          T                 T                  T

Do you know if there is a software to do it? samtools?

alignment
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updated by Biostar Biostar • written by shinken123 shinken123

1 answer

sam2tsv : https://github.com/lindenb/jvarkit/wiki/SAM2Tsv

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written by Pierre Lindenbaum Pierre Lindenbaum

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