VCF comparison: shared variants
Hi! Is there a way to compare two vcf not only by position, but also for the genotypes? I want to extract from two vcf files the variants shared by both individuals, having not only the same position but also the same genotype. Thanks
• 1,231 views
•
link
updated
by
Biostar
•
written
by
deniselavezzari •
•
written
by
deniselavezzari •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Perform mean imputation
written by Patrick •
-
Tabix position and alternative allele
written by deniselavezzari •
-
Finding shared genotypes between multiple VCF files
written by ccagg
-
How to apply vcftools --diff to identify vcf-specific variants/records
written by Shicheng Guo
-
compare and merge VCF files
written by qwzhang0601
-
extract SNPs present only in one individual and not in all the others from a multisample vcf file
written by elena.paesini •
-
Indel concordance from different VCF files
written by tejaswikoganti
-
Vcf-compare two multi-sample vcf files
written by AB
-
vcftools comparison by individual/sites
written by qzbu •
-
Remove positions that are non-variant in a subset of samples from a vcf file
written by Aliaksei Holik
merge your VCFs and filter. https://www.google.com/search?q=how+to+merge+vcf+site%3Abiostars.org
You can try this tool: https://github.com/imgag/ngs-bits/blob/master/doc/tools/SampleSimilarity/index.md