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-   -   Substantial change in TS VariantCaller default parameters (http://seqanswers.com/forums/showthread.php?t=88988)

r.rosati 04-25-2019 02:07 PM

Substantial change in TS VariantCaller default parameters
 
Hi all,
please be aware that Thermo did some very substantial changes in the default VariantCaller parameters for germline exomes in TS version 5.10. For example, the default "Germline low stringency" parameters for the 540 chip now require a minimum coverage of 40 reads for indels, 30 for MNPs and 35 reads for SNPs. If you're using default parameters with VariantCaller, these changes are likely affecting you; and if you expected to call variants at a depth of 20 reads or more, be aware that this is no more the case. You will lose variants at a read depth below 30.

r.rosati 05-24-2019 12:43 PM

I really thought this thread would get more traction.


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