I have a question about a quirk of the VCF output by samtools (0.1.18) mpileup.
In some cases insertions are reported with two or more bases in the reference sequence, for example:
It was my impression that the reference sequence existed only to say "the insertion happened after this point", and so I don't understand why it's necessary to include any preceding bases, the C in this case, rather than simply reporting it as:
Is there some significance to this that I am missing?
In some cases insertions are reported with two or more bases in the reference sequence, for example:
Code:
Chr1 1790 . CA CAA 117 . INDEL;...
Code:
Chr1 1791 . A AA 117 . INDEL;...
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