Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • adaigle
    replied
    I know this post is several months old and you've hopefully figured it out by now, but I have a similar question I'm hoping someone else will stop by.

    Here is the answer to your question I found in a helpful mpileup tutorial (link): “We don’t want to trust SNPs at sites with super high coverage, because they might be represent variation between variable copy number repeats, i.e., the reads that map to this location in the reference are actually from duplicated sites in your sample; you can–and should–change this parameter based on the kind of coverage you have in your dataset, e.g., -D500.”

    What I'm wondering is how exactly you figure out what number to use? Is there any rule of thumb for what to do with your coverage information to know how many reads are too many?

    Hope you figured your stuff out

    Leave a comment:


  • eric.fuchs
    started a topic Read Depth in varFilt -D

    Read Depth in varFilt -D

    Hello all,

    I'm new to bioinformatics and I'm trying to teach myself most of these things.

    I just called snp's with samtools and mpileup. I then proceeded to filter using:

    bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf

    I'm a bit confused on why I should worry about filtering on *maximum* read depth rather than on minimum. Shouldn't I select a minimum read depth and allow for the maximum to go as high as possible? Could this lead to other sorts of trouble?

    Thanks for help or redirecting me to the proper source,

    Eric,

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
38 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
61 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X