Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • skblazer
    Member
    • Feb 2009
    • 51
    #1

    How to call SNPs via samtools for sex-chromosome of diploid species

    Hi,

    I want to call SNPs for the sex chromosomes but autosomes via samtools for one diploid individuals.

    samtools mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
    bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf

    The SNP frequency of sex-chromosome is half of the autosomes, so I think maybe I need change some parameters?
    Tags: None
    • skblazer
      Member
      • Feb 2009
      • 51
      #2
      Help, please......

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
          by SEQadmin2




          NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
          Yesterday, 06:46 AM
        • SEQadmin2
          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
          by SEQadmin2



          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating          ...
          10-14-2026, 09:55 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:57 AM
        0 responses
        27 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:57 AM  
        Single-Cell Sequencing of 5 Million Immune Cells Links Genetic Variants to Disease by SEQadmin2
        Started by SEQadmin2, 10-28-2026, 09:51 AM
        0 responses
        18 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-28-2026, 09:51 AM  
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        71 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 11:13 AM  
        Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        48 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        View All
        Working...