How could I get population or individual specific genotypes from multi sample VCF file
I build a neighbour-joining tree from a multi-sample (genotype) vcf file and could see the population structure in the samples. I was wondering if I could extract population-specific variant/genotype information from vcf file (present in one population but absent in other).
• 1,901 views
•
link
written
by
nagarsaggi •
1 answer
so you want to extract GT from subsets of samples from your VCF ? If yes use bcftools view -S sample_list.txt input.vcf > subset.vcf where sample_list.txt is a text file containing the list of sample id you want to extract (one sample id per line).
• 0 views
•
link
written
by
Nicolas Rosewick
Log in to answer this question.
More posts like this
-
Add reference genomes as an outgroup to a phylogenetic tree
written by Álvaro •
-
how to extract variants from the vcf.gz files linked below?
written by Mahad •
-
How to remove homozygous reference genotypes from multi-sample vcf file based on a threshold
written by kk.mahsa
-
Extracting variants from genic region
written by nagarsaggi •
-
Use of GenotypeGVCFs in population genetic studies
written by kk.mahsa
-
Finding Variants Unique to a Subset of Samples in a Multi-Sample VCF File
written by Abhishek •
-
sorting a multi-sample (genotype) vcf file
written by nagarsaggi •
-
extract SNPs present only in one individual and not in all the others from a multisample vcf file
written by elena.paesini •
-
extracting genotypes from a multi-sample VCF that have certain variants
written by Floydian_slip
-
Is that possible to use Neighbor Joining algorithm for a distance matrix with more than 1M taxa
written by ajingnk
