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brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
141 stars 54 forks source link

YC and YD tags #94

Open YettaWang opened 3 months ago

YettaWang commented 3 months ago

Hello, could you tell me what the YC and YD tags mean? I need to use an analysis tool compatible with Bismark, and perhaps I can generate the XR and XG tags from these two tags. This is very urgent, and I am eagerly awaiting your response

Javkhaa commented 2 months ago

Hello, could you tell me what the YC and YD tags mean? I need to use an analysis tool compatible with Bismark, and perhaps I can generate the XR and XG tags from these two tags. This is very urgent, and I am eagerly awaiting your response

So I have been looking into this and from the source code 

        # first letter of chrom is 'f' or 'r'
        direction = aln.chrom[0]
        aln.chrom = aln.chrom[1:]

        assert direction in 'fr', (direction, aln)
        aln.other.append('YD:Z:' + direction)

It seems YD represents what XG tag in Bismark and YC is what XR tag represent.