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Is it possible, supported, and documented? Or should I just close and re-open? Thank you that solved it!


Karina Borlaug Kopi: I doubt that BAQ is the cause, as it should only reduce quality values and never increase them. You might instead be seeing the result of the overlap detection. This changes the quality values in read pairs where the forward and reverse reads are long enough to overlap each other. Barcode Printer CN-244C that happens, the lower-quality base in the pair will Barcode Printer CN-244C set to zero and the higher-quailty one to the sum of the two original quality values if they agree, or to 0. The Sanger Institute http: On Mon, 17 JunKarina Borlaug wrote: James Bonfield Emne: I tried this command instead: However as you point out it might be more valuable to keep the BAQ.

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I am trying to extract the quality values with a python script in order to create a frequency plot. However when viewing the same. If you add the "-B" option you'll probably see the qualities you expect, however this may not be what you want. See https: James -- James Bonfield jkb On Fri, Jun 14, at Hi I am Barcode Printer CN-244C some inconsistency in the samtools mpilup.


Here I observe the ascii characters: Subset of the basequality column: BB; Please let me know if you need more info Regards Karina. The htsjdk code doesn't implement reference-less compression and I also don't see any code paths where it generates 'b' Barcode Printer CN-244C.

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A bit late, but Barcode Printer CN-244C just noticed by accident where I use the 'b' feature. It just stores the sequence as-is. It can be useful for assemblies where the "reference" is ephemeral and it's pointless lodging a copy with a refget server although in practice we're better off embedding the reference instead. Example command line "scramble -x in.

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I don't know how this related to Mark Duplicates, but it's possible a similar cause triggers it there. Does htsjdk support that".

Maybe it's become misaligned due to some process and rather than create a whole string of SNPs it's created "b" features instead? I'm guessing this must be htsjdk as my code doesn't take that approach, even though it may well be a better strategy. Buy Carbon Ribbon For Taiwan Barcode Printer CN-244C CNC Barcode Label Printer Enhanced Wax-based Ribbon at Stylebest Store with high quality & fast delivery. Amazing shop Carbon Ribbon For Taiwan TSC CNC Barcode Label Printer Enhanced Wax-based Ribbon today now.


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