Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Variant calling with GATK between two cell lines

    I recently got some whole genome sequencing data from my platform that would constitute some validation data for my other RNA-seq data. The idea was that the platform would do all the bioinformatic analyses for this data, so that I could keep my focus on RNA rather than DNA, but it turns out that they don't routinely do the last part of the analysis that I want: finding any differing mutations between my two sample types. I now have to do that myself, so I come here for help.

    I have two isogenic cell lines, theoretically differing in a single mutation, and that is what we want to confirm (or that, at least, any other mutatations are in non-functional or otherwise non-relevant regions). As far as I understand it, the platform has done the alignment and the heaviest parts of the analysis, as well as a variant calling relative the reference. I'm really only interested in the difference between the cell lines, and not between cell lines / reference.

    I was pointed towards the GenotypeGVCFs function of GATK. If I understand it correctly, what I do is input my two samples GVCFs and run it. I'm not sure why I need a reference, though. I made some rudimentary code:

    Code:
    java -jar GenomeAnalysisTK.jar \
    	-T GenotypeGVCFs \
            -nt 16 \
    	-R .../human_g1k_v37.fasta \
    	--variant .../sample1.clean.dedup.recal.bam.genomic.vcf \
    	--variant .../sample2.clean.dedup.recal.bam.genomic.vcf \
    	-o .../output.vcf
    Is this what I'm looking for? If not, what am I missing, or am I completely off course?

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
67 views
0 likes
Last Post seqadmin  
Working...
X