Best tool to merge .vcf files from different variant callers?
I have vcfs from the same samples that have variants called from one of three callers. I want to put these files together so that I can annotate them together. Is there a known best way to do this?
• 1,754 views
•
link
updated
by
Biostar
•
written
by
j.lunger18 •
•
written
by
j.lunger18 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
written by JourneyToAbyss
-
How best to classify consensus SVs merged from multiple callers
written by eebloom •
-
merging structural variants from various callers into one vcf file (long read sequencing)
written by Shaghayegh •
-
Annotate variants for cancer genomics studies
written by epigene
-
Merge vcf files from the four variant callers from TCGA
written by j.lunger18 •
-
How to extract reads that support the structural variants using the vcf file and bam file?
written by Venkatesh Chellappa •
-
Concat VCFs with some shared samples
written by QVINTVS_FABIVS_MAXIMVS
-
Merge vcf files of structural variants
written by ma17 •
-
Merging VCFs: Illumina/GATK and LoFreq
written by ari.nazarian •
-
Combine single sample vcfs together
written by sumudu_rangika •
You're looking for
bcftools concat(manual). I don't think combining calls from different callers is recommended though.