Reprocess recent SP runs without merging

[AmandaBirmingham]

From: Rob Knight
Date: Friday, August 13, 2021 at 1:59 PM
Subject: Re: SP Runs

That’s great, thanks so much! What are the chances CCBB might be able to run these in the next week or two?

Thanks,
Rob

On Aug 13, 2021, at 1:52 PM, Jepsen, Kristen wrote:

These runs are the latest that are the same samples run over 2 lanes: (we didn’t do any in June/July so I grabbed May also)
210511_A00953_0299_BH7KLJDRXY
210529_A00953_0312_BHFGFYDRXY
210529_A00953_0313_AHFGT7DRXY
210803_A00953_0367_AHC5WFDRXY
210806_A00953_0372_BHCMVCDRXY
Kristen Jepsen, PhD

On Aug 12, 2021, at 9:24 PM, Rob Knight wrote:

Thanks, Peter — Kristen let’s define “recent” as “all SP covid runs since June 1”?

The specific comparisons we have in mind are:

• concordance between lane 1 and lane 2 in terms of variant calls and pass/fail threshold
• concordance between either lane and (lane 1 and lane 2 merged) in terms of variant calls and pass/fail threshold

We want to know if there is a systematic difference between the two lanes in the flow cell, and also if the results are essentially (say >99%) the same using one lane versus using two lanes.

Thanks,
Rob

On Aug 12, 2021, at 9:21 PM, DeHoff, Peter wrote:

Hi Kristen,
The results from the individual files from the recent SP lanes looked to be about the same in each lane and about the same when the data was combined. This may indicate that we can get away with less sequencing depth for the samples. Can you prepare a list of recent SP runs that Amanda can parse to run the CCBB pipeline as individual lanes? This will help to determine what, if any, tradeoffs exist by cutting the depth by about 50%. Thank you.

Peter De Hoff, PhD