VarScan shift in counting of bases!

SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

For a list of the official rules, visit (https://www.seqanswers.com/forum/sit...wledge-and-win)

See less

AlbertZANG

Junior Member

Join Date: Jun 2012

Posts: 2
- Share
- Tweet
#1

VarScan shift in counting of bases!

06-18-2012, 10:29 AM

I'm using VarScan.v2.2.11.

The problem I'm reporting here is something about VarScan's parameter --min-avg-qual when using command mpileup2indel. I'm setting it to be default, which is 15.

In the input pileup file:
CHROMOSOME_I 221154 g 42 .,,,,,,,+1c,+1c,,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c,+1c.+1C,+1c.+1C,+1c,+1c,+1c,+1c.+1C.+1C,+1c,+1c,+1c.+1C,+1c,+1c,+1c.+1C.+1C.+1C.+1C.+1C 1C?C<FFFFDHJEAJDJIJG<JJG'GIDIJBD9JDDDG?FDF

The corresponding output:
CHROMOSOME_I 221154 G +C */+C:41:8:34:45.33%:4.4044E-13 Pass:11:30:10:24:1E0 0 1 0 0 */+C:41:8:34:45.33%:4.4044E-13

The red colored part of the input won't get passed the --min-avg-qual filteration, because it's base quality is less than 15. The prblem is that in the output, we see the Cov=41 (which is correct), Reads1=8 (which is also correct), but Reads2=34 (which should be 33, because one of the insertion has mapping quality less than 15).

Anyone has a similar problem like me? Could anyone help? I think this might be a bug of VarScan.
Tags: mpileup, varscan

Previous template Next

A Review of Next-Generation Sequencing Methods for Studying Epigenetics—Part 1

by seqadmin

Developments in sequencing technologies and methodologies have transformed the field of epigenetics, giving researchers a better way to understand the complex world of gene regulation and heritable modifications. This article explores some of the diverse sequencing methods employed in the study of epigenetics, ranging from classic techniques to cutting-edge innovations while providing a brief overview of their processes, applications, and advances.

Methylation Detect...
- Channel: Articles
05-31-2023, 10:46 AM
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

Topics	Statistics	Last Post
Genetic Discoveries Transform Our Understanding of Primate Diversity and Behavior by seqadmin Started by seqadmin, Yesterday, 08:56 PM	0 responses 8 views 0 likes	Last Post by seqadmin Yesterday, 08:56 PM
Deep Sequencing Unearths Novel Genetic Variants: Enhancing Precision Medicine for Vascular Anomalies by seqadmin Started by seqadmin, Yesterday, 07:33 AM	0 responses 8 views 0 likes	Last Post by seqadmin Yesterday, 07:33 AM
Unveiling Genetic Associations Through Transcription Factor Binding Quantitative Trait Loci by seqadmin Started by seqadmin, 05-31-2023, 07:50 AM	0 responses 4 views 0 likes	Last Post by seqadmin 05-31-2023, 07:50 AM
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

Header Leaderboard Ad

VarScan shift in counting of bases!

Announcement

SEQanswers June Challenge Has Begun!

VarScan shift in counting of bases!

Latest Articles

ad_right_rmr

News