Comments (3)
Hi Paul,
This appears to be a problem with some of your VCF entries, specifically the ORIGINAL_MUTECT_FILTER
INFO field. This INFO field is defined like this:
##INFO=<ID=ORIGINAL_MUTECT_FILTER,Number=1,Type=String,Description="Original MuTect FILTER string">
i.e., a String field with exactly one value. However some of your VCF variants look like this
1 1560892 . C A . PASS BAFP=99;BAFP_NORMAL=9;ECNT=1;HCNT=36;MAD_LEFT_OFFSET=8.00;MAD_RIGHT_OFFSET=0.00;MAX_ED=.;MEDIAN_LEFT_OFFSET=12.00;MEDIAN_RIGHT_OFFSET=75.00;MIN_ED=.;NLOD=37.79;ORIGINAL_MUTECT_FILTER;TLOD=59.21;TLOD_FWD=23.42;TLOD_REV=35.80;TUMOR_SB_POWER_FWD=0.999;TUMOR_SB_POWER_REV=1.000;CSQ=A|intron_variant|MODIFIER|MIB2|ENSG00000197530|Transcript|ENST00000505820.2|protein_coding||7/19|ENST00000505820.2:c.1210-34C>A|||||||||1||HGNC|30577||||||MAGALRRGRALGSRPSGPTVSSRRSPQCPVAQEGLGARSRPRVAPRSLARCGPSSRLMGWKPSEARGQSQSFQASGLQPRSLKAARRATGRPDRSRAARPTMDPSAHRSRAAPPNMDPDPQAGVQVGMRVVRGVDWKWGQQDGGEGGVGTVVELGRHGSPSTPDRTVVVQWDQGTRTNYRAGYQGAHDLLLYDNAQIGVRHPNIICDCCKKHGLRGMRWKCRVCLDYDLCTQCYMHNKHELAHAFDRYETAHSRPVTLSPRQGLPRIPLRGIFQGAKVVRGPDWEWGSQDGGEGKPGRVVDIRGWDVETGRSVASVTWADGTTNVYRVGHKGKVDLKCVGEAAGGFYYKDHLPRLGKPAELQRRVSADSQPFQHGDKVKCLLDTDVLREMQEGHGGWNPRMAEFIGQTGTVHRITDRGDVRVQFNHETRWTFHPGALTKHHSFWVGDVVRVIGDLDTVKRLQAGHGEWTDDMAPALGRVGKVVKVFGDGNLRVAVAGQRWTFSPSCLVAYRPEEDANLDVAERARENKSSLSVALDKLRAQKSDPEHPGRLVVEVALGNAARALDLLRRRPEQVDTKNQGRTALQVAAYLGQVELIRLLLQARAGVDLPDDEGNTALHYAALGNQPEATRVLLSAGCRADAINSTQSTALHVAVQRGFLEVVRALCERGCDVNLPDAHSDTPLHSAISAGTGASGIVEVLTEVPNIDVTATNSQGFTLLHHASLKGHALAVRKILARARQLVDAKKEDGFTALHLAALNNHREVAQILIREGRCDVNVRNRKLQSPLHLAVQQAHVGLVPLLVDAGCSVNAEDEEGDTALHVALQRHQLLPLVADGAGGDPGPLQLLSRLQASGLPGSAELTVGAAVACFLALEGADVSYTNHRGRSPLDLAAEGRVLKALQGCAQRFRERQAGGGAAPGPRQTLGTPNTVTNLHVGAAPGPEAAECLVCSELALLVLFSPCQHRTVCEECARRMKKCIRCQVVVSKKLRPDGSEVASAAPAPGPPRQLVEELQSRYRQMEERITCPICIDSHIRLVFQCGHGACAPCGSALSACPICRQPIRDRIQIFV GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:27,18:0.400:9:9:0.500:1099,657:14:13 0/0:127,0:0.00:0:0:.:5082,0:59:68
specifically, note how the ORIGINAL_MUTECT_FILTER
is only ORIGINAL_MUTECT_FILTER;
. This doesn't match the field definition. If it matched it would look like ORIGINAL_MUTECT_FILTER=some_filter;
. I'm not sure what tool might be populating this field but I assume that variants like the above does not have a mutect filter set. In those cases this field should just be absent from the INFO fields.
from vatools.
Dear Susan,
Thanks so much! I could not see the problem to save myself.
I replaced entries as you suggested and no problems.
Thanks again for getting back so quickly.
Cheers
Paul
FYI the entries were put in using a GATK walker. I think the error occurs when the filter is "." originally. So yes its a custom annotation that cased the problem
from vatools.
You're welcome. I will be closing this ticket but do feel free to reopen should you run into any additional problems.
from vatools.
Related Issues (20)
- Enhancement: Adding allele counts per strand in vcf-readcount-annotator HOT 1
- warn when pick flag is expected but not observed
- Add feature to vcf-genotype-annotator to allow for adding GT field to existing samples
- Inaccurate warning message when running vcf-expression-annotator
- Bug in "vcf-genotype-annotator" due to misspelling HOT 1
- vcf-readcount-annotator only annotates first variant for indel HOT 1
- getting error when The INFO field name to use HOT 4
- When running the vcf-info-annotator support input TSVs with multiple value columns
- AttributeError: 'bool' object has no attribute 'split' HOT 2
- vep_annotation_reporter.py + AttributeError: 'bool' object has no attribute 'split' HOT 3
- ref_transcript_mismatch_reporter: `ValueError: invalid literal for int() with base 10: '71/98'`
- VAtools vcf-expression-annotator does not add gene expression for genes without annotated gene names HOT 2
- small special bug about logging
- Installation via pip requires version previous than 21 because of Python version HOT 2
- VEP entry for at CHR chr*, POS *, REF *, ALT * already exists HOT 2
- ValueError: invalid literal for int() with base 10 HOT 1
- Support for GZ compressed annotation files
- Please consider adding support for multi-thread support HOT 3
- Support gene names as well as gene Ensembl IDs when using the `custom` option of the `vcf-expression-annotator` HOT 4
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 vatools.