Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Brian Bushnell
    replied
    If you are interested in indels, particularly very long deletions that are common in cancer, I recommend mapping with BBMap, which outperforms everything on indel accuracy. There's also a thread for it, here:
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    As for what you call variations with, I'm not sure what's best. GATK and samtools pileup are commonly used. Just make sure that whatever tool you use does NOT reassemble or realign indel-containing reads, because it will probably do a worse job than BBMap's raw output.

    Leave a comment:


  • Looking for tools for calling snv and indel(Somatic Variant)

    Dear expert,
    I am working on exome-seq data.
    Looking for tools for calling snv and indel(Somatic Variant) in matched tumor-normal samples. Any suggestions?
    Thank you very much in advance.

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM
  • seqadmin
    The 3D Genome: New Technologies and Emerging Insights
    by seqadmin


    The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

    Basic Organization and Structure
    Understanding...
    01-22-2024, 03:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:57 AM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
402 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-09-2024, 03:36 PM
0 responses
646 views
0 likes
Last Post seqadmin  
Working...
X