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Confusion over newer Mutect2 tutorial,
Dear Mutect team,
At the start of this link it says that this tutorial had been deprecatedhttps://software.broadinstitute.org/gatk/documentation/article?id=11136
while the newer documentation of version 22.214.171.124 here (
does not recommend GetPileUpSummaries and Calculate contamination steps. This gives an impression that these steps are not needed in version 126.96.36.199. But when I proceed to the FilterMutectCalls (188.8.131.52) programs, it still requires contamination table.
Can you please help me by clarifying that do we still need to perform Step 3 from the old tutorial (184.108.40.206) while using 220.127.116.11?