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Add RNU-gene and reference files cleanup #231

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Sep 26, 2024
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Add RNU-gene and reference files cleanup #231

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17d2103
Update reference tools structure and update config to new version
Jakob37 Sep 24, 2024
6d02f51
Logging to distinguish what is new and what is all added from ClinVar…
Jakob37 Sep 26, 2024
5e6597e
Changelog
Jakob37 Sep 26, 2024
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26 changes: 17 additions & 9 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,18 +1,26 @@
# Files
git.hash
nextflow.config
todo
mito_full.nf

# Suffix
*~
__pycache__/
container/*.sif
*.sif
.nextflow*
nextflow.config
work/
*.html
*#
git.hash
todo
mito_full.nf
## ref tools
bin/reference_tools/*.log
bin/reference_tools/*.bed
*.orig

# Folders
__pycache__/
work/
data/
.vscode/

# Ref tools
bin/reference_tools/*.log
bin/reference_tools/*.bed
bin/reference_tools/refdata/*.vcf.gz

0 ...e_tools/agilient_hg38_nochr_noalt_1-3.bed → ...refdata/agilient_hg38_nochr_noalt_1-3.bed
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1 change: 1 addition & 0 deletions bin/reference_tools/refdata/user_added.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
17 43387226 43387417 RNU2-4
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@alkc alkc Sep 25, 2024 •
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Coordinates check out 👍

338 changes: 0 additions & 338 deletions bin/reference_tools/update_bed.pl
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2 changes: 1 addition & 1 deletion configs/nextflow.hopper.config
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Expand Up @@ -113,7 +113,7 @@ profiles {
params.outdir = "${params.resultsdir}${params.dev_suffix}"
params.subdir = 'wgs'
params.crondir = "${params.outdir}/cron/"
params.intersect_bed = "${params.refpath}/bed/wgsexome/exons_108padded20bp_clinvar-20231230padded5bp.bed"
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Checked the diffs using bedtools intersect -a <> -b <> -v, confirming that the changes was some added ClinVar (~1000), a few removed, and the added RNU-gene (please double check as a reviewer)

Sure about that ~1000 added, or is it a typo? I get 168 new entries when comparing the new file with the old:

(alkc-base) alkc@MTLUCMDS1:~$ bedtools intersect -a /fs1/resources/ref/hg38//bed/wgsexome/exons_108padded20bp_clinvar-20240825padded5bp.bed -b /fs1/resources/ref/hg38//bed/wgsexome/exons_108padded20bp_clinvar-20231230padded5bp.bed -v | wc -l     
168                                                                                                                                                                                                                                                   
(alkc-base) alkc@MTLUCMDS1:~$ bedtools intersect -b /fs1/resources/ref/hg38//bed/wgsexome/exons_108padded20bp_clinvar-20240825padded5bp.bed -a /fs1/resources/ref/hg38//bed/wgsexome/exons_108padded20bp_clinvar-20231230padded5bp.bed -v | wc -l     
33

RNU confirmed added w/ correct corrdinated:

(alkc-base) alkc@MTLUCMDS1:~$ bedtools intersect -a /fs1/resources/ref/hg38//bed/wgsexome/exons_108padded20bp_clinvar-20240825padded5bp.bed -b /fs1/resources/ref/hg38//bed/wgsexome/exons_108padded20bp_clinvar-20231230padded5bp.bed -v | grep RNU  
17      43387226        43387417        RNU2-4

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Sure about that ~1000 added, or is it a typo? I get 168 new entries when comparing the new file with the old:

Here is the log output:

INFO: Clinvar in common between versions: 231560
INFO: Added new (unique targets): 42111 (1305)
INFO: Removed old (unique targets): 18330 (37)

But, this comparison is between the ClinVar vcfs, not between the final intersect files. Maybe most of the new entries are overlapping with the exons.

I'll see if I can verify that hypothesis.

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OK, I understand this now. The logged numbers are for targets added and removed to the bed file based on the new ClinVar, i.e. what isn't present in the exons, agilient and our custom bed.

I think the number is correct, but I'll see if I can clarify the code / output a bit so this is clear next time around.

I'll re-request review when I am done with this.

params.intersect_bed = "${params.refpath}/bed/wgsexome/exons_108padded20bp_clinvar-20240825padded5bp.bed"
params.align = true
params.varcall = true
params.annotate = true
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