How does Picard basecalling make decisions on NovaSeq data?
Answered
b) What does (......) mean?
Hello, I've been starting to work with some data our lab has generated from NovaSeq S4 runs, and I was surprised to see mixed basecalls in the data (e.g. W for an A or T). I know the CBCL files are only using two bits for their basecalls so they can't call a W.
Where does this call come from/how does Picard know to make it? This has implications for our pipeline when we are trying to match barcodes at a certain hamming distance.
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Hm. It's possible I'm just misreading some code in the lab (or the files were mislabeled/undocumented). Maybe Picard is not doing this after all?
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Hi James Webber,
I'm not sure exactly which Picard tool you are using. Could you fill in the details from here if you still want help from the GATK Support team?
Thank you!
Genevieve
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I figured out was going on and it was unrelated to Picard. It was just using IlluminaBasecallsToSam and I thought it was producing these odd basecalls, but it was actually a downstream part of the pipeline I was using that was not initially obvious to me.
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Okay, thanks for the update James Webber! Glad you found the issue.
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