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Usage of DenoiseReadCounts in PerformSegmentation
One of our collaborators wanted to compare the differences between the outputs of
ModelSegments (in GATK 4.1) and
PerformSegmentation (in GATK 4.0b6). The tooldocs, however, was not particularly clear whether the output of
DenoiseReadCounts(in GATK 4.1) can be used in
PerformSegmentation, as the archived
NormalizeSomaticReadCounts doc wasn't very specific about how it performs normalization.
Can the GATK team please confirm the following:
1. Can the output of
DenoiseReadCounts be used as the
-TN input in
2. Even if (1) is positive, are the outputs of
DenoiseReadCounts mathematically equivalent to that of
NormalizeSomaticReadCounts, provided the same PON is used?
Thanks a lot for your help!