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IUPAC nucleotide codes (picard)
I am trying to use picard (tool: FastqToSam) where the non-standard letter 'X' have been introduced (for reasons not relevant for the question) but picard thows an exception - perhaps expected:
Exception in thread "main" java.lang.IllegalStateException: Bad base passed to charToCompressedBaseHigh: X(88) in read: FUN-EAS999R:999:KC987CH:1:11:138:280
-Is there an option to allow X's ?
-Alternatively, which uipac nucleotide codes are accepted other than ACTGN ?