knausb/vcfR

Issues

• vcfR2tidy: behavior when > 1 record at same chrom/POS

  #214 opened 2 months ago by gevro
  12

• See sequence length

  #213 opened 7 months ago by jenifferteles
  1

• How to avoid to print the vcfR header?

  #191 opened 3 years ago by Shicheng-Guo
  2

• read.vcfR() not recognizing missing data

  #207 opened 2 years ago by loukiaspi
  3

• change genotype(change gap to NA)

  #212 opened 2 years ago by snackens
  2

• vcfR Subsetting to the first chromosome

  #211 opened 2 years ago by charbel2998
  1

• Filtering for minor allele Frequency

  #204 opened 2 years ago by mattbareno
  4

• compilation issue

  #209 opened 2 years ago by knausb
  2

• Hide a panel from chromoqc or plot

  #210 opened 2 years ago by NowickiLab
  2

• chromR object not finding DP and MQ values

  #206 opened 2 years ago by JuanitaGil
  2

• extract.gt() missing heterozygotes

  #208 opened 2 years ago by samarth8392
  1

• vcfr, extract.gt, bcftools, vcf format incompatible?

  #189 opened 3 years ago by wbsimey
  6

• Assign_Indiv_by_Geno.R function of Demuxafy.sif problems with the vcf

  #205 opened 2 years ago by ElenaSLuis
  1

• write.vcf() not filtering variants

  #203 opened 2 years ago by mattbareno
  2

• gene/chromosome annotation

  #202 opened 2 years ago by umasstr
  2

• vcfR2tidy can't handle files with empty INFO

  #200 opened 2 years ago by alkaZeltser
  4

• Rename Genotype information

  #199 opened 2 years ago by Flavjack
  2

• Heterozygous SNP calling

  #197 opened 2 years ago by ettorefedele
  15

• read.vcfR() coredump with empty lines in input

  #198 opened 3 years ago by ntakebay
  5

• vcfR not recognizing all chromosomes

  #196 opened 3 years ago by lukaskon
  2

• RStudio Session aborted when writing VCF

  #195 opened 3 years ago by eibol1
  0

• How can I add population information to genind converted using vcfR2genind?

  #194 opened 3 years ago by kopelol
  2

• Error: ID column contains non-unique names

  #193 opened 3 years ago by bathycy
  1

• Variants with MAF of 0 after removing monomorphics

  #192 opened 3 years ago by Neato-Nick
  6

• 0 percent missing data

  #190 opened 3 years ago by redgcko7
  2

• Combine Two Variants In One Single VCF File

  #187 opened 3 years ago by gk7279
  2

• does it support vcf comes from vep or vardict

  #188 opened 3 years ago by worker000000
  1

• Unable to convert to long-format using vcfR2tidy

  #186 opened 3 years ago by oisinmccaffrey
  0

• Understanding genetic_diff() number of alleles output

  #185 opened 3 years ago by EveTC
  4

• error while accessing filltered vcf file

  #184 opened 3 years ago by sekhwal
  1

• sex determination

  #182 opened 4 years ago by AnjaliC4
  8

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

  #183 opened 4 years ago by hope-data-science
  2

• Convert vcfR object to tabular format

  #181 opened 4 years ago by Al-Murphy
  3

• Adding INFO tags on the basis information in the INFO tags

  #180 opened 4 years ago by misrak
  4

• is.polymorphic bug, returns FALSE for a sample of all hets?

  #178 opened 4 years ago by JimWhiting91
  9

• Subset or downsample a VCF file?

  #179 opened 4 years ago by vertesy
  2

• How to work with multiple vcf files?

  #177 opened 4 years ago by zh-zhang1984
  2

• overlapping sliding window

  #176 opened 4 years ago by michaeljmetzger
  2

• After using read.vcfR file format is not recognised * This is not a vcf!

  #175 opened 4 years ago by frederikvand
  0

• vcfR reading INFO/DS field

  #174 opened 4 years ago by meixilin
  1

• Read depth can not be plotted from VCF file

  #173 opened 4 years ago by AG-Run
  1

• Error in extract.gt(vcf) - ID column contains non-unique names

  #172 opened 4 years ago by gimeno99
  2

• CRAN not supporting vcfR

  #165 opened 4 years ago by jonathan-velotta
  9

• Put gt back to vcf

  #171 opened 4 years ago by zoeluo15
  2

• vcfR: ID column contains non-unique names

  #170 opened 4 years ago by gimeno99
  7

• not available for R4.0

  #169 opened 4 years ago by complexgenome
  4

• s3read_using lasts forever reading a VCF file

  #167 opened 4 years ago by HediaTnani
  1

• cannot install for R version 4 on Mac

  #168 opened 4 years ago by brockels
  3

• read.vcfR randomly dropping genotypes

  #166 opened 4 years ago by akijarl
  2

• Impending CRAN retirement?

  #163 opened 4 years ago by katiesaund
  3