MouseContamEstimator is a simple python script for end users to estimate mouse contamination level of their WES samples.
Based on the HAMAlist, it calculates the median of VAFs for all HAMAs in your WES data.
The only library dependency for this script is NumPy.
MouseContamEstimator takes tsv formatted output of GATK CollectAllelicCounts as input.
Therefore, in order to perform the estimation, the result file of CollectAllelicCounts should be generated as follows.
gatk CollectAllelicCounts \
-I $AlignedPath$SAMPLE.bam \
-R $REF \
-L $INTERVAL \
-O $AnalysisPath$SAMPLE.allelicCounts.tsv
The usage of MouseContamEstimator is simple as follows.
python MouseContamEstimator $AnalysisPath$SAMPLE.allelicCounts.tsv
Under revision.