how to see 2 or more variants are in the same read

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that girl

• November 28, 2020 09:29

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).

 

how can I see a germline or simatic variant is in the same read?

thanks a lot

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  that girl

  • November 29, 2020 00:08

  here I am asking how to know that in gatk vcf

  thanks a lot

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