Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • VarScan early halt

    Hi,

    I'm new to VarScan. I was trying to call copynumber from my exome sequencing data.

    My script is
    samtools mpileup -q 1 -f ~/hg19.fa normal.rmdup.bam tumor.rmdup.bam | java -Xmx4g -jar ~/VarScan.v2.3.3.jar copynumber > output --mpileup 1

    It seems to run the first bit of the program and start to generate 2 files
    1. copynumber
    But it halted when it went to
    chrM 16066 16165 100 53.7 89.7 0.740 1.0

    The other file 30.copynumber only has the column name
    chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio gc_content

    Running message is as following:
    [mpileup] 1 samples in 2 input files
    <mpileup> Set max per-file depth to 8000
    Min coverage: 10
    Min avg qual: 15
    P-value thresh: 0.01
    Reading input from STDIN
    Reading mpileup input...
    Parsing Exception on line:
    chrM 16184 C 0 0
    8

    It seems that something happened at the site chrM 16184... But I used my bam files to call SNPs/coverage from gatk and they worked out fine... I didn't know what's wrong...

    Many thanks,
    John

  • #2
    John,

    I would restructure your command slightly so that redirecting the output is the last thing you do... VarScan might not be interpreting your "--mpileup 1" :
    samtools mpileup -q 1 -f ~/hg19.fa normal.rmdup.bam tumor.rmdup.bam | java -Xmx4g -jar ~/VarScan.v2.3.3.jar copynumber --mpileup 1 > output

    If this doesn't help, I believe the issue occurs at a position where you have 0x coverage... those usually aren't present in pileup files. Please send me the mpileup lines for chrM from positions 16180- 16190 and I'll take a look.

    Feel free to post here or e-mail to dkoboldt (at) genome [dot] wustl [dot] edu

    Comment


    • #3
      Hi, all !

      Though this thread had been posted about one year ago, I'd like to share my recent experience in meeting the same error in using Varscan2.
      The causal thing would be the inconsistent of samtools version in generating BAMs and producing mpileup files.
      In my case, input BAMs were generated by samtools-0.1.18 in weeks ago, while now the samtools version in my PATH is 0.1.19, and the error arised if I don't specify to use the samtools-0.1.18 in generating pileup file.

      Thanks a bunch!

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Strategies for Sequencing Challenging Samples
        by seqadmin


        Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
        03-22-2024, 06:39 AM
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 03-27-2024, 06:37 PM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-27-2024, 06:07 PM
      0 responses
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      53 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      69 views
      0 likes
      Last Post seqadmin  
      Working...
      X