Unique mutations between VCF files
I have two VCF files that are using hg38 as the reference genome. I am trying to find unique mutations between the two vcf files. What program should I use for this? I tried using vcfunique from vcflib, but was having serious installation issues. It does not work on windows, so I tried using a virtual linux machine, but I can't get it to work.
• 1,047 views
•
link
updated
by
Ram
•
written
by
kshaffman •
•
written
by
kshaffman •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How do I use md5sum to check if my .fastq files from SRA Explorer have been downloaded correctly
written by biotrekker •
-
Virtual box
written by georgeof35 •
-
Error while using VCFtools (--maf) to filter by allele frequency
written by kshaffman •
-
Using bcftools isec without stripping meta data and outputting as a VCF
written by kshaffman •
-
How to use vcfuniq from vcflib?
written by kshaffman •
-
Biobakery virtual machine installation
written by anjalivasudevan98 •
-
Error when trying to use Ensembl virtual machine
written by langziv •
-
Files recognized as gzip but not compressed
written by beaferbl •
-
Strange, FastQC doesn't work on windows, any suggestions?
written by seta
-
Splitting .vcf file
written by zizigolu
Do you have a prefered environment (R, python, etc.)? You could even do this with a one line command in awk or bash, but to do that you'd have to know a bit more about your VCF files (e.g. are they single sample or multisample VCFs).
Hi, the VCF files I am working with are each single sample files. My preferred environment is python, it is the only language I know anything about, but I'd be willing to use a different language.