Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Correct options for CNVnator

    Greetings,

    I'm trying to run CNVnator on a cohort of ~300 BAM files.

    For testing purposes I'm trying to run it on just 3 BAM files first.
    Here are the commands I'm running:

    Code:
    export HS37d5=/data/fastas/hs37d5
    
    cnvnator -root chr22.root -genome GRCh37 -chrom 22 -tree \
    	/nfs/wgs30x/bam.files/samp1.bam \
    	/nfs/wgs30x/bam.files/samp2.bam \
    	/nfs/wgs30x/bam.files/samp3.bam;
    
    cnvnator -root chr22.root -genome GRCh37 -chrom 22 -his 1000 -d $HS37D5
    
    cnvnator -root chr22.root -genome GRCh37 -chrom 22 -stat 1000
    
    cnvnator -root chr22.root -genome GRCh37 -chrom 22 -partition 1000
    
    cnvnator -root chr22.root -genome GRCh37 -chrom 22 -call 1000 > chr22.cnvnator.out

    Now all of this runs and I don't get an error (as far as I can tell).
    The last command I try is:

    Code:
    cnvnator -pe /nfs/wgs30x/bam.files/samp1.bam \
       /nfs/wgs30x/bam.files/samp2.bam \
       /nfs/wgs30x/bam.files/samp3.bam \
       -qual 20 -over 0.8 -root chr22.root -f chr22.support_reads;
    This command never finishes. I left it running for 36 hours and it didn't produce anything.

    I believe I'm screwing up the cnvnator -pe command but I can't figure out what the correct command should be.

    Using the cnvnator2VCF.pl produces a VCF file but it doesn't contain any read count information.

    Does anyone have any suggestions as to what I'm doing wrong?
    In case it helps I'm using CNVnator v0.4 (latest download from github).
    The system is a RHEL 7.2 box fully patched.

    Thank you in advance for any and all help.

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, Yesterday, 06:37 PM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X