Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • IgorFobia
    Junior Member
    • Jan 2010
    • 6

    #1

    VarScan readcounts command gives error with mpileup

    I am trying to run VarScan with readcounts option, but I keep getting this error

    Reading input from /users/fg253/new_data_drug_resistance/Co89-2/remapping_to_reference/out.sorted.rmdup.bam.mpileup
    Error: Invalid format for pileup at line null
    EK12AG100 1438119 T 0
    This is the command I'm using:
    java -jar $SW_DIR/VarScan.v2.3.6.jar readcounts $MPILEUP --min-base-qual 20 --output-file $READCOUNTS_VCF
    Can you please help me?
    Thanks

Latest Articles

Collapse

  • 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
  • SEQadmin2
    New Genomics Technologies Take Aim at Long-Standing Limits
    by SEQadmin2


    Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

    We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing
    ...
    09-28-2026, 10:25 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by SEQadmin2, Yesterday, 11:13 AM
0 responses
19 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, Yesterday, 10:48 AM
0 responses
18 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-15-2026, 10:52 AM
0 responses
36 views
0 reactions
Last Post SEQadmin2  
Started by SEQadmin2, 10-14-2026, 05:39 AM
0 responses
42 views
0 reactions
Last Post SEQadmin2  
Working...