-
Not an answer to your question, but interesting read considering IndelRealigner: https://software.broadinstitute.org/gatk/blog?id=7847 -
Hi Guillaume,
The correction appends if there is a better alignment possible, how do you know you should have a different alignment in this position ?
TristanLeave a comment:
-
using GATK IndelRealigner
Hi,
I have some difficulties using IndelRealigner on my data. After comparing bam files before and after realignement process I find some regions where a correction should have occured. (an igv capture of an ambiguous region that isnt resolved after realignement : https://postimg.org/image/7yuy0hz81/ ). Is it normal that all my indels "problems" are not solved? And are there parameters to adjust to solve them? Have I made mistakes running the commands?
(here are my command lines ) java -Xmx12000m -jar ~/Soft/GATK/GenomeAnalysisTK.jar -T RealignerTargetCreator -nt 15 -R ~/igv/genomes/genome.fa -I sample.bam -o temp.indel.intervals java -Xmx12000m -jar ~/Soft/GATK/GenomeAnalysisTK.jar -T IndelRealigner -R ~/genome.fa -I sample.bam -targetIntervals temp.indel.intervals -o sample_realigned.bam
I'm willing to take any ideas!
-
Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM
Leave a comment: