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IUPAC nucleotide codes (picard)

provirusprovirus DenmarkMember

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
at htsjdk.samtools.BAMRecordCodec.encode(
at htsjdk.samtools.BAMFileWriter.writeAlignment(
at htsjdk.samtools.SAMFileWriterImpl.close(
at picard.sam.FastqToSam.doWork(
at picard.cmdline.CommandLineProgram.instanceMain(
at picard.cmdline.PicardCommandLine.instanceMain(
at picard.cmdline.PicardCommandLine.main(

-Is there an option to allow X's ?

-Alternatively, which uipac nucleotide codes are accepted other than ACTGN ?



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