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.
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.
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