Announcement

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

  • SNPsaurus
    replied
    So this has 2 reads of the reference, but converts to a no call? Do other loci with only reads get called? There may be a firm threshold for needing >2 reads to support a call. GQ is 0, so that means alternative genotypes are equally likely. I'd say if other loci get called at 2 reads then you need to visualize the alignments to see what is going on.

    Leave a comment:


  • Negin
    replied
    @SNPsaurus, yes the output is a gvcf file (almost same as vcf file), and it has all the information that you mentioned. Here, is an example of one locus in one sample with no call.

    eg. NC_000913 4473651 . C <non_ref> . . . GT:AD: DP:GQ:PL 0:2,0:2:0:0,0

    and after combining with other samples and genotyping it with GASTK4, it will change to this:

    GT:AD: DP:GQ:PL .:0,0:0:.:0,0
    Last edited by Negin; 09-12-2019, 06:47 AM.

    Leave a comment:


  • SNPsaurus
    replied
    What is the output? A vcf file will typically give the genotype call and then report on read depth, allele depth, genotype probabilities and quality scores for the call, mapping, and sequences. Can you manually inspect the GATK output? You can also load the bam file into a genome viewer and inspect the region of interest.

    Leave a comment:


  • Negin
    replied
    Thanks @SNPsarus, but do you know also how can I solve it via GATK?

    Leave a comment:


  • SNPsaurus
    replied
    I like breseq http://barricklab.org/twiki/bin/view...meResequencing because it shows the evidence for each variant call and highlights regions of no coverage as well.

    Leave a comment:


  • Negin
    started a topic no call in gvcf file of bacteria samples

    no call in gvcf file of bacteria samples

    I used GATK 4 for variant calling in bacteria samples. For some samples and some variants, there is no call. How can I know this no call is because of low-quality or gene absence?

Latest Articles

Collapse

  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
    ...
    02-08-2024, 06:33 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Today, 08:52 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 08:57 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
428 views
0 likes
Last Post seqadmin  
Working...
X