wrong STR thresholds in STR-report

[tamara-nano]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v2.0.0-g52e3698

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

Hello!

When running the STR-workflow on epi2me I noticed that I've got some wrong thresholds for the pathogenity of some str-expansions in the report. There it seems that the threshold is set to the base count and not the repeat count. These are HG002-data.

F.ex. PABPN1: normal max: 10 repeats, pathogenity starts at 11 repeats. Here the threshold is set at base 11 and not repeat 11, you see in both alleles only 6 repeats (fig: hg002) Also one allele has a wrong repeat-count (?) In the mapping you see 6/6 repeats for both alleles. This happened with a few repeats. It also enforces a repeat count when one allele is missing. Mapping of PABPN1

RFC1: normal repeat range 11-200 repeats, pathogenity 400 - >2000 repeats (source GeneReviews), also wrong threshold (fig: hg002 with 12/115 repeats for both alleles, ref-hg38 has 11 rep )

Please could you have a look into this and check the thresholds?

Else I find this pipeline pretty convenient with a nice report-output! Great work!

Best, Tamara

Relevant log output

-

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

No response

[vlshesketh]

Hi @tamara-nano, thank you for your positive feedback on the workflow! I will review the STR reporting script and get back to you shortly.

[vlshesketh]

Hi @tamara-nano apologies for the delay - you are correct that the plotting script is using the wrong value for the normal max. and pathogenic min. in the repeat content plot. I will update the ticket when a fix is released.

[vlshesketh]

Hi @tamara-nano, this has now been fixed in v2.2.0.