recalibration using second base call for Illumina

[drio]

Do you know any software or publication that uses/describes the benefits of recalibrating illumina data using the second base calls?

Have you done any experiment with this? If so, how are you saving the
second base call in your pipelines? I don't think the current SAM spec has room for it.

I see some potential on this to increase the SNP call quality specially under low coverage but I haven't seen any data.

[nilshomer]

Do you know any software or publication that uses/describes the benefits of recalibrating illumina data using the second base calls?

Have you done any experiment with this? If so, how are you saving the
second base call in your pipelines? I don't think the current SAM spec has room for it.

I see some potential on this to increase the SNP call quality specially under low coverage but I haven't seen any data.

See the "S2" tag, which encodes the probabilites on the other three bases. I have not read papers that utilize them but I know of people who are considering methods.