% Depth at X vs cumulative_coverage_proportions

lletournlletourn montrealMember
edited December 2014 in Ask the GATK team

Hello,
I'm trying to understand why gte_25 != %_bases_above_25

sample_summary->%_bases_above_25 == 88.6%

sample_cumulative_coverage_proportions->gte_25 == 0.91

I would expect both to be identical but they never are.

They are always close though.

There is something in the calculation that eludes me.

Thanks
Louis

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Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @lletourn‌

    Hi Louis,

    I think the issue is the slight difference in wording. The sample_summary gives you the percent of bases above 25, whereas the sample_cumulative_coverage_proportions gives you the percent of bases greater than or equal to 25.

    So, in your example, %_bases_above_25 should equal gte_26.

    I hope this helps. I was confused for quite some time myself!

    -Sheila

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