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Hi, I have SAM files where the there are = signs for matching nucleotides. Is there an easy way (i.e. using samtools) to convert these to the corresponding ACTG letters? It is confusing GATK UnifiedGenotyper and I cannot find any SNPs. |
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Might this Picard method help? I saw it mentioned on the mailing list at some point. Alec Wysoker said: "The Picard project contains a (not very well tested) method for constructing a reference string from read bases, CIGAR and MD: net.sf.samtools.util.SequenceUtil.makeReferenceFromAlignment()" |
