Hi everyone, I am trying to use mpileup(samtools) for variant calling. In my results which happens to be a VCF file, I get " X" in alt column. The documentation on mpileup says that "In the BCF generated by SAMtools, an non-ref base 'X' represents an base has not been seen from the alignment data. Such a base is necessary to evaluate the probability of missing a non-ref allele due to sampling fluctuation." I do not know how to fix this error. Can someone please help. Your help would be much appreciated. Thanks :) PS: I am using mpile up in galaxy and not on command line.
Question: MPile up Result contains "X" in Alt column
13 months ago by
Bioinformatician_in_trouble • 10 wrote:
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