Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Conflict between mpileup/bcftools and GATK in VCF file

    I'm using samtools mpileup | bcftools view to generate VCF files for reads mapped to a mitogenome reference. I would like to use the GATK VariantsToTable walker to create an importable table of the base distribution and qualities at each site. The problem I'm having is that for sites with coverage below 3 (DP=1 or DP=2), the VCF file that gets created has an 'X' in the ALT field rather than a '.'. When I put these files through GATK's VariantsToTable, I get the following error:

    ##### ERROR MESSAGE: The provided VCF file is malformed at line nmber 27: Unparsable vcf record with allele X

    Here are some example lines from my VCF file:

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT z0000064_mtdna-test
    gi|170027011|gb|EU557096.1| 17 . T X 0.404 . DP=1;AF1=0;AC1=0;DP4=0,1,0,0;MQ=23;FQ=-8.25 GT:PLP:GQ 0/0:0,3,23:1:13
    gi|170027011|gb|EU557096.1| 18 . T X 0.206 . DP=2;AF1=0;AC1=0;DP4=1,1,0,0;MQ=31;FQ=-10.9 GT:PLP:GQ 0/0:0,6,60:2:19
    gi|170027011|gb|EU557096.1| 19 . T . 16.2 . DP=3;AF1=0;AC1=0;DP4=1,2,0,0;MQ=27;FQ=-13.7 PLP 0:3
    gi|170027011|gb|EU557096.1| 20 . T . 16.2 . DP=3;AF1=0;AC1=0;DP4=1,2,0,0;MQ=27;FQ=-13.7 PLP 0:3

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
11 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