vcfR
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knausb
Tools to work with variant call format files
Adds a CHROM param to `create.chromR` to allow the user to designate which chromosome should be subset instead of defaulting to the first. This includes appropriate warnings about mismatched names...
This is similar to issue #107. We would like an interface where one can specify chromosome + region, and obtains only the parts of the VCF that correspond to this...
Hello - I have annotated my VCF files with VEP. I love the vcfR2tidy function which parses out the vcf file into different data frames for visualization and downstream analysis....
@knausb hope this make the issue clear R version 3.6.2 (2019-12-12) on HPC clusters require(vcfR) vcf
Hi Brian, When using `vcfR2genlight()` with a very small dataset, the function may set different ploidy for each sample. This behavior comes from the automatic determination of the ploidy when...
I am processing VCF file to split the columns until the INFO field (columns 1-9) into tab separated columns. The example input has 250K variants. To do this i am...
Hello Brian, I'm using SLiM 3 to generate vcf files which I am analysing in R, however occasionally read.vcfR() was causing my R session to 'encounter a fatal error' and...
Hi Brian, I found another unexpected behavior when using `vcfR2DNAbin()` which is not related to #122. When data have indels with missing data and these indels are kept, a DNAbin...
Excellent package! I have prototyped a few solutions to use this to apply ML classification of called variants and do filtering. This is more of a feature request. Just wanted...
Hi Thanks for an awesome package. We work on a series massive low-coverage WGS dataset (>100 million sites, ~1000 samples), which (from what I can tell) prevents in-memory computation on...
