Low read consensus with GroupReadsByUmi

Question

[a.palmer]

Hi everyone,

I’m trying to troubleshoot a low read consensus rate in duplex sequencing data - by using GroupReadsByUmi and CallDuplexConsensusReads in the fgbio package.

For CallDuplexConsensusReads, I use:

java -jar fgbio-1.4.0.jar CallDuplexConsensusReads \
    --input=grouped.bam --output=consensus.unmapped.bam \
    --error-rate-pre-umi=15 --error-rate-post-umi=10 \
    --min-input-base-quality=10

But get:

[2021/12/06 17:33:10 | CallDuplexConsensusReads | Info] Raw Reads Filtered Due to Not Enough Reads (Either Total, AB, or BA): 20,787,008 (0.9964).

When looking at ‘grouped.bam’, I noticed the MI tag only referred to two consecutive sequences, presumably these are the paired reads. Also, each pair has the same read identity (MI= N/A& N/A, not N/A & N/B).

Example from grouped.bam:

A00133:442:HM5MFDSX2:3:2615:27823:2895  83      1       3050000 60      29S71M  =       3050000 -71     AATGTTTTGCCAGTTCTTTTAAATTCTCAACAGTAAAAGAAACAAATTTTAGAGGAACTAAAATATTGCAATCTCCATGCCATGGGAGAATAGAAATACA   FFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF          ZA:Z:CGG ZB:Z:AAT        MC:Z:24S71M50S  MD:Z:0N70       PG:Z:bwa        RG:Z:A  MI:Z:0/B        NM:i:1  MQ:i:60 UQ:i:37                                       AS:i:71  RX:Z:CGG-AAT

A00133:442:HM5MFDSX2:3:2615:27823:2895  163     1       3050000 60      24S71M50S       =       3050000 71      TTTGCCAGTTCTTTTAAATTCTCAACAGTAAAAGAAACAAATTTTAGAGGAACTAAAATATTGCAATCTCCATGCCATGGGAGAATAGAAATACATACCGAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGG      FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFF:,FFFFF:FFFFFFFF:FFFFFFFFF      ZA:Z:CGG        ZB:Z:AAT                                      MC:Z:29S71M      MD:Z:0N70       PG:Z:bwa        RG:Z:A  MI:Z:0/B        NM:i:1  MQ:i:60 UQ:i:37 AS:i:72 RX:Z:CGG-AAT

A00133:442:HM5MFDSX2:3:1468:3821:33786  99      1       3050000 60      21S124M =       3050014 159     GCCAGTTCTTTTAAATTCTCAACAGTAAAAGAAACAAATTTTAGAGGAACTAAAATATTGCAATCTCCATGCCATGGGAGAATAGAAATACATCTATCAGAGATATTGTCAGGACCCGAAAGAAATGAAACCCAAAGTGGAGGTC      FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      ZA:Z:CGA        ZB:Z:CTA       MC:Z:145M                              MD:Z:0N123       PG:Z:bwa        RG:Z:A  MI:Z:1/A        NM:i:1  MQ:i:60 UQ:i:37 AS:i:124        RX:Z:CGA-CTA

A00133:442:HM5MFDSX2:3:1468:3821:33786  147     1       3050014 60      145M    =       3050000 -159    AAATTTTAGAGGAACTAAAATATTGCAATCTCCATGCCATGGGAGAATAGAAATACATCTATCAGAGATATTGTCAGGACCCGAAAGAAATGAAACCCAAAGTGGAGGTCCACTAGTGAGTATAATGATGGCAGGTATTTTTGCT      FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF      ZA:Z:CGA        ZB:Z:CTA       MC:Z:21S124M                           MD:Z:145 PG:Z:bwa        RG:Z:A  MI:Z:1/A        NM:i:0  MQ:i:60 UQ:i:0  AS:i:145        RX:Z:CGA-CTA

I think this is why the consensus rate is so low (from a lack of reads with the same MI), though I’m not sure.

For reference, this is my GroupReadsByUmi code:

java -jar fgbio-1.4.0.jar GroupReadsByUmi \
    --input=mapped.bam --output=grouped.bam \
    --strategy=paired --edits=1 --min-map-q=1

There was suitable amplification in the original sequencing experiment, so there must be an ample number of reads for grouping by UMI.

Thanks for your help!

Alex