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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(BAMRecordCodec.java:161)
at htsjdk.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:143)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:226)
at picard.sam.FastqToSam.doWork(FastqToSam.java:355)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:269)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:98)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:108)

-Is there an option to allow X's ?

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



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