Find mismatch position/read in STAR SAM file

[Panagiotis Alexiou]

I am trying to find mismatch positions in the results files produced by STAR aligner.

The CIGAR string doesn't contain mismatch positions and there is no MD:Z tag (similar to BWA aligner).

I know the nM tag shows the number of mismatches, but I want to know the position of the mismatch on the genome (and preferably the genomic nucleotide and read nucleotide).

This capability is crucial for calling SNPs.

Please advise if I am missing something obvious.

[Alexander Dobin]

Hi Panagiotis,

to get this attributes please use the latest STAR patch with the following option:

--outSAMattributes NH HI NM MD

Cheers

Alex