Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Merging SNPs and indels VCF from strelka for ANNOVAR annotation

    Hello,

    as part of my analysis workflow I'm using Strelka to compare sample pairs, and this results in two files, one for SNPs and one for Indels. For the purpose of annotation (and to show them to the rest of the laboratory) I would like to merge them in a single VCF and then annotate the results with ANNOVAR.

    I know the GATK's CombineVariants can do the job, but I'm phasing out GATK usage unless absolutely required, and it feels way too "heavy" to use it just to merge two VCFs.

    I looked at vcf-merge from vcftools, but apparently it doubles the VCF header when merging the two files (it keeps information from both, even if identical), and ANNOVAR can't cope with that (it will not convert the results to its own format).

    For reference, what I used was:

    Code:
    vcf-merge passed.somatic.indels.vcf.gz passed.somatic.snvs.gz > comparisoname.vcf
    Where both files have been already compressed and indexed with tabix.
    If I use vcf-concat, the resulting file is readable by ANNOVAR, but I don't think I'm doing the right thing (as I'm just pushing things on top of each other).

    Any suggestions I could use to merge these files?

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
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 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