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* We recommend to check each lane for the possibility of sample swaps. When [SELF-IBD] << 1 AND [%MIX] ~ 0, then it is possible that the sample is swapped with another sample. When [BEST-IBD] ~ 1, [BEST_SM] might be actually the swapped sample. Otherwise, the swapped sample may not exist in the genotype data you have compared against.
* We recommend to check each lane for the possibility of sample swaps. When [SELF-IBD] << 1 AND [%MIX] ~ 0, then it is possible that the sample is swapped with another sample. When [BEST-IBD] ~ 1, [BEST_SM] might be actually the swapped sample. Otherwise, the swapped sample may not exist in the genotype data you have compared against.
* When genotype data is not available but allele-frequency-based estimates of [%MIX] >= 0.03 and [BESTMIXLLK-] is large (greater than 100), then it is possible that the sample is contaminated with other sample. We recommend to use per-sample data rather than per-lane data for checking this for low coverage data, because the inference will be more confident when there are large number of bases with depth 2 or higher.
* When genotype data is not available but allele-frequency-based estimates of [%MIX] >= 0.03 and [BESTMIXLLK-] is large (greater than 100), then it is possible that the sample is contaminated with other sample. We recommend to use per-sample data rather than per-lane data for checking this for low coverage data, because the inference will be more confident when there are large number of bases with depth 2 or higher.
* If [EXHET] << 1.00, it indicates that the sequence reads have excessive homozygosity, and this might probably be due to the small library size. In this case, we recommend to check the duplication rate of the BAM file, for example, using samtools flagstat, and see whether the library size is too small to call heterozygous sites appropriately.
== Command Line Options ==
== Command Line Options ==
