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understanding dcov option

blueskypyblueskypy Member ✭✭
edited December 2016 in Ask the GATK team

Here is an excerpt of the docs of -dcov option:
"For read-based traversals (ReadWalkers like BaseRecalibrator), it controls the maximum number of reads sharing the same alignment start position."

Here are my questions:
1. which are ReadWalkers? for example, is IndelRealigner a read walker?
2. For a read walker, if read length is 100 bp, does "-dcov 1" mean the max depth at any locus is 100?


Best Answer


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