vcfR

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read.vcfR() coredump with empty lines in input

5

Hi, I noticed that read.vcfR("test.vcf") caused core dump (and R quits) with the following error: /usr/include/c++/11/bits/stl_vector.h:1045: std::vector::reference std::vector::operator[](std::vector::size_type) [with _Tp = std::__cxx11::basic_string; _Alloc = std::allocator; std::vector::reference = std::__cxx11::basic_string&; std::vector::size_type =...

ntakebay

Error: ID column contains non-unique names

1

When I try to run vcfR on a vcf file I have I keep running into the same error when I try to extract the GT from the Genotype Section...

bathycy

How to avoid to print the vcfR header?

2

How to avoid to print the vcfR header? It gives me some trouble for further analysis to the log files. Thanks ``` ***** *** vcfR *** ***** This is vcfR...

Shicheng-Guo

does it support vcf comes from vep or vardict

1

Thanks for this wonderful tool, does it support parse vcf comes from vep or vardict

worker000000

Understanding genetic_diff() number of alleles output

4

Hello I am somewhat confused by the output by `geneitc_diff()`, in particular the number of alleles in each population. Given the example data below: ``` library(vcfR) data(vcfR_example) myPops

EveTC

sex determination

8

Hi, Thanks for this very cool tool! Could you please suggest a way to determine sex of every sample in vcfR? One approach I know is heterozygosity rate on chrX....

AnjaliC4

About vcfR::heatmap.bp, is there a way to scale the heatmap but keep the barplot as sum of unscaled values?

2

The heatmap produced by heatmap.bp is really beautiful, is there a way to scale the rows but keep the barplot to summarise the raw data? Thanks.

hope-data-science

overlapping sliding window

2

This is great! Currently it appears that the windows are non-overalpping (ie. 1-1000, 1001-2000, 2001-3000, etc). I was wondering if you have developed any way to modify the method to...

michaeljmetzger

vcfR reading INFO/DS field

1

Hi, Thank you so much for making this amazing software possible! I think there might be a small bug regarding reading the `INFO` field when the gene annotations field including...

meixilin

Convert vcf with varying ploidy level

16

Hello, I imported `vcf` containing diploids and tetraploids as `data_vcf

V-Z