Comments (4)
There are a few reasons why certain variants are skipped.
- The reference file has a mismatch with what's in the ClinVar data
- The reference file used has the reference sequence soft-masked in lower-case, causing a pseudo-mismatch. Because of this line https://github.com/ericminikel/minimal_representation/blob/master/normalize.py#L80 this case results in an "Incorrect REF value" warning being generated and the variant skipped. I have a fork of
normalize.py
which makes the reference bases uppercase: https://github.com/kristjaneerik/minimal_representation/blob/uppercase-ref/normalize.py#L80 - If the REF and ALT alleles are the same or an invalid nucleotide is seen
- There's no SequenceLocation information in the ClinVar XML, so we don't know where the variant is
However, I see this particular variant in clinvar_with_exac.tsv.gz
(line 46777), clinvar.vcf.gz
(line 46822) and clinvar.tsv.gz
(line 46777) when zgrep
-ing for 92130876
in these files that are currently in the repo.
from clinvar.
Hello kristjaneerik !
Thank you for your response, I was checking several variants and here is the one that I have not found there (I have searched on ready built TSV files):
7 99382096 rs2740574 C T
Another problem is that when I was trying to run the pipeline (inregarldess of using your normalize.py fork or original some) I have got the errors (listed below).
Can you please tell me what is wrong with my environment? Or probably FASTA selection (I've tried different reference fastas from UCSC and 1000g, but no success).
[Dec 8 19:23:53]: --> Exec 1.4: Rscript join_data.R variant_summary.txt.gz
[Dec 8 19:23:53]: Output (last mod N/A): clinvar_combined.tsv [doesn't
exist yet]
[Dec 8 19:23:59]: [1] 184803 14
[Dec 8 19:24:12]: Warning message:
[Dec 8 19:24:12]: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
[Dec 8 19:24:12]: embedded nul(s) found in input
[Dec 8 19:24:12]: [1] 354889 30
[Dec 8 19:24:12]: Error in [.data.frame
(x, r, vars, drop = drop) :
[Dec 8 19:24:12]: undefined columns selected
[Dec 8 19:24:12]: Calls: subset -> subset.data.frame -> [ -> [.data.frame
[Dec 8 19:24:34]: $subset(txt_download, assembly == "GRCh37", select = desired_columns)
[Dec 8 19:24:34]: <environment: 0x222f190>
[Dec 8 19:24:34]:
[Dec 8 19:24:34]: $subset.data.frame(txt_download, assembly == "GRCh37", select = desired_colu
[Dec 8 19:24:34]: <environment: 0x222de20>
[Dec 8 19:24:34]:
[Dec 8 19:24:34]: $x[r, vars, drop = drop]
[Dec 8 19:24:34]: <environment: 0x2396f20>
[Dec 8 19:24:34]:
[Dec 8 19:24:34]: $``[.data.frame(x, r, vars, drop = drop)
[Dec 8 19:24:34]: <environment: 0x2396f58>
[Dec 8 19:24:34]:
[Dec 8 19:24:34]: $`stop("undefined columns selected")`
[Dec 8 19:24:34]: <environment: 0x2352348>
[Dec 8 19:24:34]:
[Dec 8 19:24:34]: attr(,"error.message")
[Dec 8 19:24:34]: [1] "Error in `[.data.frame`(x, r, vars, drop = drop) : \n undefined columns selected\nCalls: subset -> subset.data.frame -> [ -> [.data.frame\n"
[Dec 8 19:24:34]: attr(,"class")
[Dec 8 19:24:34]: [1] "dump.frames"
[Dec 8 19:24:34]: Finished 1.4. Running time: 0:00:41.048258 sec.
[Dec 8 19:24:34]: WARNING: unable to rename tmp.2016-12-08_19.23.51.clinvar_combined.tsv to clinvar_combined.tsv. tmp.2016-12-08_19.23.51.clinvar_combined.tsv is not readable
[Dec 8 19:24:34]: --> Skipping 1.5: (cat clinvar_combined.tsv | head -1 > tmp.2016-12-08_19.23.51.clinvar_combined_sorted.tsv ) && (cat clinvar_combined.tsv | tail -n +2 | egrep -v "^[XYM]" | sort -k1,1n -k2,2n -k3,3 -k4,4 >> tmp.2016-12-08_19.23.51.clinvar_combined_sorted.tsv ) && (cat clinvar_combined.tsv | tail -n +2 | egrep "^[XYM]" | sort -k1,1 -k2,2n -k3,3 -k4,4 >> tmp.2016-12-08_19.23.51.clinvar_combined_sorted.tsv )
[Dec 8 19:24:34]: Input (last mod N/A): clinvar_combined.tsv [Error - input file not found]
[Dec 8 19:24:34]: Traceback (most recent call last):
[Dec 8 19:24:34]: File "/root/.local/lib/python2.7/site-packages/pypez.py", line 769, in does_command_need_to_run
[Dec 8 19:24:34]: try: raise Exception("File not found: " + str(input_filename))
[Dec 8 19:24:34]: Exception: File not found: clinvar_combined.tsv
[Dec 8 19:24:34]:
Thanks in advance,
Peter
from clinvar.
With regards to 7 99382096 rs2740574 C T
: yes, it is not in any of the posted files. When I fetch from the genome I used, that position shows up at c
-- so this variant was (most likely) skipped due to softmasking.
The issue you are seeing (join_data.R
failing, which triggers other failures downstream) is because ClinVar changed their data format and this codebase hasn't been updated to deal with it as the change is not a simple one. See #18 , #19. The solution for now, unfortunately, is to use older files as outlined in those issues. There's nothing wrong with your environment as such, you just need to specify an older XML and summary table as in #19 .
I don't know if/when the original authors will get to address this join_data.R
issue; I have some thoughts on what could be done, but might not have the time to do it.
from clinvar.
#21 from @XiaoleiZ has fixed join_data.R so we'll be making up-to-date releases again.
from clinvar.
Related Issues (20)
- Sometimes "symbol" disagrees with primary hgvs gene annotation HOT 1
- Missing variants HOT 4
- RScript crash HOT 1
- Feature request: Including strand info and genomic start and end coordinates HOT 1
- Wrong gene mapping HOT 2
- Add "last_evaluated" field to VCF
- Improper handling of pseudoautosomal region HOT 1
- Improper labelling of conflicting variants as pathogenic HOT 3
- Job parse failure on system execution. ENV issues? HOT 5
- Another translation for gold stars
- Add LICENSE HOT 2
- Need to Update pathogenic & conflict boolean regex. HOT 1
- ClinSig changes for some halpotypes in join_data.R - become wrong! HOT 2
- Clinical Significance Order Lost in Allele Grouping HOT 8
- Convert the pipeline to hail for .tsv processing steps?
- Augmented tables in output HOT 2
- missing clinvar_alleles_with_exac_v1.*.tsv.gz HOT 1
- Mismatch between clinical_significance_ordered and submitters_ordered HOT 2
- Multiple isoforms not in index
- missing hgvs_c when indel is realigned and shifted.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from clinvar.