STR (short tandem repeats) ID from bam file?

Hi all,

Are there any tools out there that are designed to extract the VNTR (variable number tandem repeats) for forensic testing from a bam file? Actually, if there was a tool that did the same from fastq it would be equally useful.

str bam

• 2,697 views • link

updated 4.2 years ago by Ram

• written 11.4 years ago by Richard

1 answer

This looks like it might be useful (Lobstr):

http://melissagymrek.com/lobstr-code/index.html

• 0 views • link

written 11.4 years ago by Richard

More posts like this

Comparing HMMER vs. HHrepID for LRR Repeat Detection and Boundary Consistency
written 1.4 years ago by jllPons •

Hi everyone! I’m currently analyzing leucine-rich repeats (LRRs) across a set of related proteins and need a reliable way to extract individual LRR units. I’m …
Similar tools to visualize pileup of long-read alignments to a STR locus
written 1.8 years ago by Antonio •

Hello everyone, I would like to ask if someone knows of tools similar to [GraphAlignmentViewer](https://github.com/Illumina/GraphAlignmentViewer) or [REViewer](https://github.com/Illumina/REViewer?tab=readme-ov-file) but for long-reads, specifically, Oxford Nanopore Technologies reads? …
Best way to add alter fastq file by adding short repeats
written 2.3 years ago by pairedttest •

Hi there I am currently working on building a tool to detect STRs in fastq files. I want to generate a dummy fastq file with …
Defining VNTR in BAM file by IGV
written 3.0 years ago by zizigolu

Hi I have `BAM` files for tumour and matched normal for my samples from WGS. By uploading `BAM` files in `IGV`, how I could know …
Question: Converting FASTQ to BAM by using Bowtie2
written 7.4 years ago by Sakhaa •

Hello everyone, I'm working on DNA data and my task generates a pipeline VCF from Fastq file, with testing different read aliner tool and different …
Short Tandem Repeats analysis
written 10.7 years ago by marina-orlova

I need to analyze 3 nucleotides tandem repeats, which tool is best in your opinion for this goal? I looked for this on Biostars but …
fastq compression tools of choice
written 10.9 years ago by Richard

Hi all, I'll be trying out a few compression tools for fastq files. So far on my list I have the following: 1. dsrc 2. …
Tool: TRAL - Tandem Repeat Annotation Library
written 10.9 years ago by Elke Schaper •

For my Ph.D., I've implemented solutions to a large number of tasks related to sequence tandem repeats. We've now decided to make the code accessible …
alt aware analysis tools?
written 11.2 years ago by Richard

Hi all, I've seen that BWA now provides some analysis tools to help take advantage of alt contigs in the the human reference. If one …
TRF output to .gff file
written 12.3 years ago by Alice

Hello, biostars! I'm trying to get .gff file from Tandem Repeat Finder output. Since TRF can't do that, I've found TRAP tool, which can create …