Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Pindel, pindel2vcf, AD for REF allele always zero?

    Hello fellow Pindel users,
    I am using Pindel to detect structural variants and I find that in output VCF files, the allele depth (AD) for the reference allele for all variants in all samples is always zero. Has anyone else experienced this or know why this might occur?

    My alignments (SAM files) were made with STAMPY.

    I am running Pindel 0.2.5 with samtools 0.1.18 with these commands:

    ../pindel -f ~/AT_Reference/TAIR10_chr_all.fa -p infile_pindel.txt -c 1 -o Chr1pin -T 12

    ../pindel2vcf -p Chr1pin_D -r ~/AT_Reference/TAIR10_chr_all.fa -R TAIR10 -d 20140901 -e 3 -mc 6 -is 72 -m 2

    I find that ALL the vcf lines in the output have support of 0 read depth for the reference allele. An example vcf line:

    1 27916160 . CATAGTAAAAGCTTTGCGTTCAGACTCTGTCTAGATGATTCAGAAAACGCTGGAAATGAACCCACTTTGCTTGGCATTTTCAATTGGTGTTTATTGGGTT CTC . PASS END=27916259;HOMLEN=0;SVLEN=-99;SVTYPE=RPL;NTLEN=2 GT:AD 1/1:0,8 1/1:0,15 1/1:0,6 1/1:0,11 1/1:0,9 1/1:0,12 1/1:0,21 1/1:0,11 1/1:0,14 1/1:0,8 0/0:0,5 1/1:0,12 1/1:0,9 1/1:0,17 1/1:0,14 1/1:0,11 1/1:0,8 1/1:0,15 1/1:0,20 1/1:0,15 1/1:0,15 0/0:0,4 1/1:0,18 1/1:0,10 0/0:0,0 1/1:0,15 1/1:0,17 1/1:0,7 0/0:0,4 1/1:0,11 1/1:0,14 1/1:0,10

    The pindel input file looks normal. Maybe there is a problem with the input STAMPY alignments?
    Any advice would be much appreciated!

  • #2
    Originally posted by BGould View Post
    Hello fellow Pindel users,
    I am using Pindel to detect structural variants and I find that in output VCF files, the allele depth (AD) for the reference allele for all variants in all samples is always zero. Has anyone else experienced this or know why this might occur?

    My alignments (SAM files) were made with STAMPY.

    I am running Pindel 0.2.5 with samtools 0.1.18 with these commands:

    ../pindel -f ~/AT_Reference/TAIR10_chr_all.fa -p infile_pindel.txt -c 1 -o Chr1pin -T 12

    ../pindel2vcf -p Chr1pin_D -r ~/AT_Reference/TAIR10_chr_all.fa -R TAIR10 -d 20140901 -e 3 -mc 6 -is 72 -m 2

    I find that ALL the vcf lines in the output have support of 0 read depth for the reference allele. An example vcf line:

    1 27916160 . CATAGTAAAAGCTTTGCGTTCAGACTCTGTCTAGATGATTCAGAAAACGCTGGAAATGAACCCACTTTGCTTGGCATTTTCAATTGGTGTTTATTGGGTT CTC . PASS END=27916259;HOMLEN=0;SVLEN=-99;SVTYPE=RPL;NTLEN=2 GT:AD 1/1:0,8 1/1:0,15 1/1:0,6 1/1:0,11 1/1:0,9 1/1:0,12 1/1:0,21 1/1:0,11 1/1:0,14 1/1:0,8 0/0:0,5 1/1:0,12 1/1:0,9 1/1:0,17 1/1:0,14 1/1:0,11 1/1:0,8 1/1:0,15 1/1:0,20 1/1:0,15 1/1:0,15 0/0:0,4 1/1:0,18 1/1:0,10 0/0:0,0 1/1:0,15 1/1:0,17 1/1:0,7 0/0:0,4 1/1:0,11 1/1:0,14 1/1:0,10

    The pindel input file looks normal. Maybe there is a problem with the input STAMPY alignments?
    Any advice would be much appreciated!
    If you extract reads and then push them through Pindel, you will not get read count for ref supporting reads. you could use -i to see whether things work out.

    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
    12 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
    52 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