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

Question

[shinken123]

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?

[cpad0112]

i guess you are asking for either gvcf or vcf. shinken123

Answer 1

[Pierre Lindenbaum]

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