Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • #1

    Insertions follow reference in vcf file

    Hi,
    I'm working with gvcf files, containing also non-variant positions. I have noticed some insertions that I'm not able to correctly interpret or handle. An example (simplified):
    Code:
    NC_013991.2 1403 . G GAA 176.32 . GT:AD:DP:GQ:PGT:PID:PL:PS ./. 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 1|1 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 ./. ./. 1/1 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. 0/0 ./. 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./.
NC_013991.2 1404 . A . . . GT:AD:DP:RGQ ./. 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 ./. ./. ./.
NC_013991.2 1405 . A . . . GT:AD:DP:RGQ ./. 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. ./. 0/0 ./. ./. ./. ./. 0/0 ./. 0/0 0/0 0/0 ./. ./. ./. ./. ./. ./. 0/0 ./. ./. ./. ./. ./. ./. 0/0 0/0 0/0 0/0 ./. ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 ./. ./. ./. 0/0 ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. ./. 0/0 ./. ./. ./.
    Here, the reference sequence is "GAA". Why, at site 1403, do I get an alternative allele "GAA"? There seem to be two samples at this position that are "1/1", thus homozygous for GAA. But they are also homozygous for A at the next positions. What thus is their genotype ? GAAAA, thus containing an insertion of AA?
    I've seen multiple cases like this, also with longer alternative alleles, and each time the alternative allele sequence exactly recapitulates the reference sequence. This seems like an error to me, but how to correct?
    The mapping was done either with bwa aln or bwa mem, and we've observed this behaviour both when using GATK4 and bcftools for genotyping.

    I would be very grateful if someone could clarify this.
    Thanks,
    Jos
    Tags: bcftools, bwa, gatk, mapping, vcf
Previous template Next

Latest Articles

Collapse
  • seqadmin
    Non-Coding RNA Research and Technologies
    by seqadmin




    Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

    Nobel Prize for MicroRNA Discovery
    This week,...
    10-07-2024, 08:07 AM
  • seqadmin
    Recent Developments in Metagenomics
    by seqadmin





    Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
    09-23-2024, 06:35 AM
View All

ad_right_rmr

Collapse

News

Collapse
Topics Statistics Last Post
Mechanical Forces in DNA Transcription Uncovered by Clemson Researchers by seqadmin
Started by seqadmin, 10-02-2024, 04:51 AM
0 responses
104 views
0 likes
 Last Post seqadmin
by seqadmin
10-02-2024, 04:51 AM  
New Epigenetic Clock Links Cheek Cells to Mortality Risk by seqadmin
Started by seqadmin, 10-01-2024, 07:10 AM
0 responses
112 views
0 likes
 Last Post seqadmin
by seqadmin
10-01-2024, 07:10 AM  
AI-Powered Blood Test Shows Promise for Early Ovarian Cancer Detection by seqadmin
Started by seqadmin, 09-30-2024, 08:33 AM
1 response
116 views
0 likes
 Last Post EmiTom
by EmiTom
10-07-2024, 06:46 AM  
Stem Cell Research Suggests Human Cells May Enter Developmental Pause by seqadmin
Started by seqadmin, 09-26-2024, 12:57 PM
0 responses
22 views
0 likes
 Last Post seqadmin
by seqadmin
09-26-2024, 12:57 PM  
View All
Working...
X