How to Fix Error in snpeff

Misbah Abbas

Junior Member

Join Date: Jun 2017

Posts: 2
- Share
- Tweet
#1

How to Fix Error in snpeff

08-09-2017, 05:36 AM

Asslamu Alikum

I am using snpeff to annotate vcf files, When I run command it gives some errors and warnings

" java -Xmx4g -jar snpEff.jar CanFam3.1.75 -v /media/misbah/dccc4c9e-df84-4f29-bd64-e6f88cf7dbce/DQ1.g.vcf > DQ1.ann.vcf"

It give error at the end of complition

ERRORS: Some errors were detected

Error type Number of errors

ERROR_CHROMOSOME_NOT_FOUND 285197

WARNINGS: Some warning were detected Warning type Number of warnings INFO_REALIGN_3_PRIME 6443 WARNING_TRANSCRIPT_INCOMPLETE 277 WARNING_TRANSCRIPT_NO_START_CODON 678825 WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME 943 WARNING_TRANSCRIPT_NO_STOP_CODON 499400 WARNING_TRANSCRIPT_NO_STOP_CODON&INFO_REALIGN_3_PRIME 346

Is it effect on the results? I don't know how to fix it.

Please tell me about it

thankx
Tags: None

Previous template Next

Differential Expression and Data Visualization: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

After covering QC and alignment tools in the first segment and variant analysis and genome assembly in the second segment, we’re wrapping up with a discussion about tools for differential gene expression analysis and data visualization. In this article, we include recommendations from the following experts: Dr. Mark Ziemann, Senior Lecturer in Biotechnology and Bioinformatics, Deakin University; Dr. Medhat Mahmoud Postdoctoral Research Fellow at Baylor College of Medicine;...
- Channel: Articles
05-23-2023, 12:26 PM
Variant Analysis and Genome Assembly: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

Continuing from our previous article, we share variant analysis and genome assembly tools recommended by our experts Dr. Medhat Mahmoud, Postdoctoral Research Fellow at Baylor College of Medicine, and Dr. Ming "Tommy" Tang, Director of Computational Biology at Immunitas and author of From Cell Line to Command Line.

Variant detection and analysis tools
Mahmoud classifies variant detection work into two main groups: short variants (<50...
- Channel: Articles
05-19-2023, 10:03 AM
QC, Alignment, and Mapping: Recommended Tools for Next-Level Sequencing Analysis

by seqadmin

With new tools and computational resources being released regularly, it can be hard to determine which are best suited for the analysis process and which older tools continue to be maintained. In an effort to assist the sequencing community, we interviewed three highly skilled bioinformaticians about their recommended tools for several important analysis applications.

Quality control and preprocessing tools
“Garbage in, garbage out” is a popular...
- Channel: Articles
05-16-2023, 10:11 AM

Topics	Statistics	Last Post
Exploring French-Canadian Ancestry: Insights into Migration, Settlement Patterns, and Genetic Structure by seqadmin Started by seqadmin, 05-26-2023, 09:22 AM	0 responses 8 views 0 likes	Last Post by seqadmin 05-26-2023, 09:22 AM
Largest Catalog of Human Protein-Coding Variation Unveiled by seqadmin Started by seqadmin, 05-24-2023, 09:49 AM	0 responses 9 views 0 likes	Last Post by seqadmin 05-24-2023, 09:49 AM
Introducing ProtVar: A Web Tool for Contextualizing and Interpreting Human Missense Variation in Proteins by seqadmin Started by seqadmin, 05-23-2023, 07:14 AM	0 responses 29 views 0 likes	Last Post by seqadmin 05-23-2023, 07:14 AM
AMP Releases Recommendations for NGS Germline Variant Confirmation by seqadmin Started by seqadmin, 05-18-2023, 11:36 AM	0 responses 113 views 0 likes	Last Post by seqadmin 05-18-2023, 11:36 AM

Header Leaderboard Ad

How to Fix Error in snpeff

Announcement

How to Fix Error in snpeff

Latest Articles

ad_right_rmr

News