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AstraZeneca-NGS / VarDict

VarDict
MIT License
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vardcit define complex variant #153

Open worker000000 opened 3 years ago

worker000000 commented 3 years ago

VarDict represents complex variant composites as a single variant, rather than as multiple individual variants. Whenever an InDel is detected in a read, VarDict will recursively scan for another InDel (within 10 bp) or mismatches (within 3 bp) in the same read, and if found, combines them as one variant. The same rule also applies to consecutive mismatches, resulting in calling multiple nucleotide variants (MNVs)

can you tell me which part of code do this, I want to learn , thanks a lot, because I do not know how to see if a variant in the same read, and I want to ask does the same read contain two conditions(1 the same read; pair end read) thanks a lot

worker000000 commented 3 years ago

image

PolinaBevad commented 3 years ago

Hi @2236529177 ,

There are few parts of code where MNV can be combined from SNVs, I will link them here: Here we look for consequent mismatches to generate MNV: https://github.com/AstraZeneca-NGS/VarDict/blob/master/vardict.pl#L1865 Here we combine it with Indels: https://github.com/AstraZeneca-NGS/VarDict/blob/master/vardict.pl#L1902 Also we check possible MNV on soft-clips: https://github.com/AstraZeneca-NGS/VarDict/blob/master/vardict.pl#L2516

Let me know if you need more details here!