Incorrect CIGAR string found. about syri HOT 6 CLOSED

Hi Yael,

You have to use the --eqx command in your minimap2 line to replace the M for X/= in your CIGAR string.

from syri.

Thanks!

from syri.

It's worth pointing out that not all SAM files come from minimap2, and 'M' is correct CIGAR under the SAM specification:

https://samtools.github.io/hts-specs/SAMv1.pdf

Therefore in my opinion this is a bug that isn't fixed.

from syri.

Syri uses CIGAR string to call SNPs and short indels. In CIGAR, M is used for both matches and mismatches, which means that using it for calling SNPs would require checking the bases in both genomes at all positions that have an M. This could result in significant computational overhead. Using =/X solves this issue as only positions with X needs to be fetched.

I am also not aware of other popular whole-genome alignment methods that do not produce SAM files with =X.

from syri.

nucmer with --sam-long produces such output. There are probably more. If you're not going to support the full CIGAR specification, it would be nice to document that under the limitations, because others might use the tool as I did, thinking that any SAM file that conforms to the specification would work.

from syri.

Documentation already shows how to generate and use alignments from minimap2 and nucmer https://schneebergerlab.github.io/syri/pipeline.html

Nevertheless, please feel free to update the documentation/code and start a pull request.

from syri.