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I am trying to understand how the MD:Z tag is used. The following is from the SAM Optional Fields Specification, which gives an example but is not thorough.

The MD field aims to achieve SNP/indel calling without looking at the reference. For example, a string ‘10A5^AC6’ means from the leftmost reference base in the alignment, there are 10 matches followed by an A on the reference which is different from the aligned read base; the next 5 reference bases are matches followed by a 2bp deletion from the reference; the deleted sequence is AC; the last 6 bases are matches. The MD field ought to match the CIGAR string.

Suppose I have a read that I want to soft clip at both ends. If the read starts with CIGAR 100M and MD 50G49, and I want to change the CIGAR to 7S86M7S, what should the MD field become?

Is there a more complete explanation of what appears in the MD tag field?

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The MD string doesn't apply to soft or hard clipped regions,. so your example read becomes 43G42. Since variant calling using something simplistic like this is only ever going to use the aligned portion, I guess there was never much reason to bother with adding in soft-clipping information. This also means that you need to parse the CIGAR string if you're using the MD string.

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