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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.
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.
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