Inconsistency in variant counts between IGV and VarScan

Hi,

I was wondering, if anyone could explain the inconsistency in read and variant counts between SAM tools/VarScan and IGV.

Thank you in advance.

alignment snp

• 1,751 views • link

updated 3.8 years ago by Ram

• written 11.0 years ago by utsavnp •

1 answer

Typically, this is due to different filtering settings in the different software packages.

• 0 views • link

updated 3.8 years ago by Ram

• written 11.0 years ago by Sean Davis

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