What is the input to Plink's distance matrix function?
I want to calculate a pairwise distance matrix (DM) on several samples (~100). When I look at Plink's documentation for calculating a DM, at no point does it seem to give a clue as to what the input file has to be. https://www.cog-genomics.org/plink/1.9/distance.
Am I missing something really obvious here?
I have a concatenated vcf for these samples. Will this suffice?
Thanks
• 2,329 views
•
link
written
by
Luther_Blisset •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Genetic distance in cM from VCF of non-reference species to run Beagle
written by Noctiluca •
-
Coded allele for plink --r command
written by Albert Henry •
-
Calculating genetic distance when some sites are ambiguous (heterozygotes)
written by emacdoug •
-
Plot PCA for .IMISS file?
written by Carla Hazel •
-
plink --indep LD calculation and filtering to VCF file in one command
written by rjzotti •
-
How to populate a column with binary values, depending on whether a sample is present in another fi…
written by Luther_Blisset •
-
PLINK - Sample(s) present with no genotype data
written by liorglic
-
PLINK - error in --make-bed
written by bsmith030465
-
How to read a ".ld.bin" file produced by PLINK
written by andreagarcia871
-
Using Plink to calculate LD between loci on different chromosomes
written by jr.azaria •
What do you mean by concatenated VCF? If you've called the variants from multiple samples in a single vcf file i.e. every sample is a column after the INFO columns, that should be enough. If not you need to use
bcftools mergeto merge your vcf files.