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Estimation of the cross-individual contamination by chromosome
We are trying to estimate the cross-individual contamination in our samples (whole genome) with ContEst and we were wondering if we could do it by chromosomes to speed up the process. We splitted the samples by chromosomes in order to perform IndelRealigner and we need them also by chromosomes to run faster MuTect1, so merging the bam files again for running ContEst would take us extra time. We understand that contamination is a global measure for the sample, but would it make sense to pass the average contamination estimation from all the chromosomes to MuTect1 instead?
Tamara and Laura