Changes

=== A guideline to interpret output files ===

=== A guideline to interpret output files ===

verifyBamID provides a series of information that is informative to determine whether the sample is possibly contaminated or swapped, but there is no single criteria that works for every circumstances. There are a few unmodeled factor in the estimation of [SELF-IBD]/[BEST-IBD] and [%MIX], so please note that the MLE estimation may not exactly match to the true amount of contamination. Here we provide a guideline to flag potentially contaminated/swapped samples  

verifyBamID provides a series of information that is informative to determine whether the sample is possibly contaminated or swapped, but there is no single criteria that works for every circumstances. There are a few unmodeled factor in the estimation of [SELF-IBD]/[BEST-IBD] and [%MIX], so please note that the MLE estimation may not always exactly match to the true amount of contamination. Here we provide a guideline to flag potentially contaminated/swapped samples  

* When [SELF-IBD] < 1 AND [%MIX] > 0 AND [REF-A2%] > 0.01, meaning 1% or more of non-reference bases are observed in reference sites, we recommend to examine the data more carefully for the possibility of contamination. Each sample or lane can be checked in this way.

* When [SELF-IBD] < 1 AND [%MIX] > 0 AND [REF-A2%] > 0.01, meaning 1% or more of non-reference bases are observed in reference sites, we recommend to examine the data more carefully for the possibility of contamination. Each sample or lane can be checked in this way.