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The function of -max_deletion_fraction argument
Just wanted to clarify about the function of -max_deletion_fraction argument for UnifiedGenotyper tool.
The documentation says:
""If the fraction of reads with deletions spanning a locus is greater than this value (0.05 byDefault) , the site will not be considered callable and will be skipped. To disable the use of this parameter, set its value to >1"".
The locus will not be considered callable only for SNVs.... correct?
Calling of deletions is ultimately regulated by the parameter -min_indel_fraction and -min_indel_count, hence, -max_deletion_fraction would not actually affect del calling....correct?