No VEP block found

[MareikeJaniak]

Hi!

I am testing out the updates in 2.1.0 and came across a behaviour I hadn't seen in the previous versions of cpsr.

With 2.1.0 (incl. the latest reference bundle), the attached input, and the following command:

cpsr --force_overwrite --secondary_findings --gwas_findings --panel_id 0 \
--input_vcf tumorPair_COLO829.ensemble.germline.vt.annot.2caller.flt.vcf.gz \
--refdata_dir $PCGR_DATA \
--vep_dir $PCGR_VEP_CACHE \
--output_dir ./cpsr \
--genome_assembly grch38 \
--sample_id tumorPair_COLO829

I'm getting this message, right before cpsr exits:

2024-10-16 09:36:43 - cpsr-summarise - INFO - CPSR - STEP 3: Cancer gene annotations with cpsr-summarise
2024-10-16 09:36:47 - cpsr-gene-annotate - WARNING - Picked VEP block for 19_5834201_C_T does not match virtual panel target genes - considering alternative consequences
2024-10-16 09:36:48 - cpsr-gene-annotate - WARNING - Picked VEP block for 19_18692362_T_G does not match virtual panel target genes - considering alternative consequences
2024-10-16 09:36:50 - cpsr-gene-annotate - WARNING - Picked VEP block for 19_50857562_C_T does not match virtual panel target genes - considering alternative consequences
2024-10-16 09:36:50 - cpsr-gene-annotate - WARNING - Picked VEP block for 19_54293995_T_C does not match virtual panel target genes - considering alternative consequences
2024-10-16 09:36:50 - cpsr-gene-annotate - INFO - NO VEP BLOCK FOUND

After poking around a bit in the code, I think what I'm seeing reflects there not being any variants of interest to include in the annotations, so no report is generated. However, I wanted to make sure that this is indeed what is going on, because the exit is somewhat abrupt and didn't happen in previous (v1) versions with this same dataset.

Thanks for your help!

Best, Mareike tumorPair_COLO829.ensemble.germline.vt.annot.2caller.flt.vcf.gz

[sigven]

I am on it , will fix:)

[sigven]

Dear Mareike, please go ahead and try the latest patch, which should fix the issue above. Let me know if you have trouble:)

best, Sigve

[MareikeJaniak]

Thanks, Sigve! I appreciate the quick response. Will try it out very shortly!

Best, Mareike

[MareikeJaniak]

Hi Sigve, Just a quick update that cpsr and pcgr are working well for us with the most recent release. Thanks for the quick response!

Best, Mareike