knausb/vcfR issues and pull requests

#214 - vcfR2tidy: behavior when > 1 record at same chrom/POS

Issue - State: open - Opened by gevro about 1 month ago - 12 comments

#213 - See sequence length

Issue - State: open - Opened by jenifferteles 6 months ago - 1 comment

#212 - change genotype(change gap to NA)

Issue - State: closed - Opened by snackens over 1 year ago - 2 comments

#211 - vcfR Subsetting to the first chromosome

Issue - State: open - Opened by charbel2998 over 1 year ago - 1 comment

#210 - Hide a panel from chromoqc or plot

Issue - State: closed - Opened by NowickiLab over 1 year ago - 2 comments

#209 - compilation issue

Issue - State: closed - Opened by knausb over 1 year ago - 2 comments

#208 - extract.gt() missing heterozygotes

Issue - State: open - Opened by samarth8392 over 1 year ago - 1 comment

#207 - read.vcfR() not recognizing missing data

Issue - State: closed - Opened by loukiaspi over 1 year ago - 3 comments

#206 - chromR object not finding DP and MQ values

Issue - State: closed - Opened by JuanitaGil over 1 year ago - 2 comments

#205 - Assign_Indiv_by_Geno.R function of Demuxafy.sif problems with the vcf

Issue - State: open - Opened by ElenaSLuis over 1 year ago - 1 comment

#204 - Filtering for minor allele Frequency

Issue - State: closed - Opened by mattbareno almost 2 years ago - 4 comments

#203 - write.vcf() not filtering variants

Issue - State: closed - Opened by mattbareno almost 2 years ago - 2 comments

#202 - gene/chromosome annotation

Issue - State: closed - Opened by umasstr almost 2 years ago - 2 comments

#201 - new feature: separation of annotation columns in tidy dataframes from VCFs annotated by snpEff or VEP tools

Pull Request - State: closed - Opened by gorgitko almost 2 years ago - 6 comments

#200 - vcfR2tidy can't handle files with empty INFO

Issue - State: open - Opened by alkaZeltser about 2 years ago - 4 comments

#199 - Rename Genotype information

Issue - State: closed - Opened by Flavjack about 2 years ago - 2 comments

#198 - read.vcfR() coredump with empty lines in input

Issue - State: open - Opened by ntakebay over 2 years ago - 5 comments

#197 - Heterozygous SNP calling

Issue - State: closed - Opened by ettorefedele over 2 years ago - 15 comments

#196 - vcfR not recognizing all chromosomes

Issue - State: closed - Opened by lukaskon over 2 years ago - 2 comments

#195 - RStudio Session aborted when writing VCF

Issue - State: closed - Opened by eibol1 over 2 years ago

#194 - How can I add population information to genind converted using vcfR2genind?

Issue - State: closed - Opened by kopelol almost 3 years ago - 2 comments

#193 - Error: ID column contains non-unique names

Issue - State: open - Opened by bathycy almost 3 years ago - 1 comment

#192 - Variants with MAF of 0 after removing monomorphics

Issue - State: closed - Opened by Neato-Nick about 3 years ago - 6 comments

#191 - How to avoid to print the vcfR header?

Issue - State: open - Opened by Shicheng-Guo about 3 years ago - 2 comments

#190 - 0 percent missing data

Issue - State: closed - Opened by redgcko7 about 3 years ago - 2 comments

#189 - vcfr, extract.gt, bcftools, vcf format incompatible?

Issue - State: closed - Opened by wbsimey about 3 years ago - 6 comments

#188 - does it support vcf comes from vep or vardict

Issue - State: open - Opened by worker000000 over 3 years ago - 1 comment

#187 - Combine Two Variants In One Single VCF File

Issue - State: closed - Opened by gk7279 over 3 years ago - 2 comments

#186 - Unable to convert to long-format using vcfR2tidy

Issue - State: closed - Opened by oisinmccaffrey over 3 years ago

#185 - Understanding genetic_diff() number of alleles output

Issue - State: open - Opened by EveTC over 3 years ago - 4 comments

#184 - error while accessing filltered vcf file

Issue - State: closed - Opened by sekhwal over 3 years ago - 1 comment

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

Issue - State: open - Opened by hope-data-science over 3 years ago - 2 comments

#182 - sex determination

Issue - State: open - Opened by AnjaliC4 over 3 years ago - 8 comments

#181 - Convert vcfR object to tabular format

Issue - State: closed - Opened by Al-Murphy over 3 years ago - 3 comments

#180 - Adding INFO tags on the basis information in the INFO tags

Issue - State: closed - Opened by misrak over 3 years ago - 4 comments

#179 - Subset or downsample a VCF file?

Issue - State: closed - Opened by vertesy over 3 years ago - 2 comments

#178 - is.polymorphic bug, returns FALSE for a sample of all hets?

Issue - State: closed - Opened by JimWhiting91 over 3 years ago - 9 comments

#177 - How to work with multiple vcf files?

Issue - State: closed - Opened by zh-zhang1984 over 3 years ago - 2 comments

#176 - overlapping sliding window

Issue - State: open - Opened by michaeljmetzger almost 4 years ago - 2 comments

#175 - After using read.vcfR file format is not recognised * This is not a vcf!

Issue - State: closed - Opened by frederikvand almost 4 years ago

#174 - vcfR reading INFO/DS field

Issue - State: open - Opened by meixilin almost 4 years ago - 1 comment

#173 - Read depth can not be plotted from VCF file

Issue - State: closed - Opened by AG-Run almost 4 years ago - 1 comment

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

Issue - State: closed - Opened by gimeno99 about 4 years ago - 2 comments

#171 - Put gt back to vcf

Issue - State: closed - Opened by zoeluo15 about 4 years ago - 2 comments

#170 - vcfR: ID column contains non-unique names

Issue - State: closed - Opened by gimeno99 about 4 years ago - 7 comments

#169 - not available for R4.0

Issue - State: closed - Opened by sariya about 4 years ago - 4 comments

#168 - cannot install for R version 4 on Mac

Issue - State: closed - Opened by brockels about 4 years ago - 3 comments

#167 - s3read_using lasts forever reading a VCF file

Issue - State: closed - Opened by HediaTnani about 4 years ago - 1 comment

#166 - read.vcfR randomly dropping genotypes

Issue - State: closed - Opened by akijarl about 4 years ago - 2 comments

#165 - CRAN not supporting vcfR

Issue - State: closed - Opened by jonathan-velotta about 4 years ago - 9 comments

#164 - Addresses issue CHROM param in create.chromR #52

Pull Request - State: open - Opened by RichardJActon over 4 years ago - 1 comment

#163 - Impending CRAN retirement?

Issue - State: closed - Opened by katiesaund over 4 years ago - 3 comments

#162 - vcfR2tidy() gives me an error: Can't combine `..1$tt` <logical> and `..2$tt` <character>.

Issue - State: closed - Opened by sridharsh over 4 years ago - 5 comments

#161 - fix #160

Pull Request - State: closed - Opened by jan-glx over 4 years ago - 6 comments

#160 - installation of master fails for missing checkbashisms

Issue - State: closed - Opened by jan-glx over 4 years ago - 7 comments

#159 - vcfR2tidy error (Can't combine `..1$tt` <logical> and `..2$tt` <character>.)

Issue - State: closed - Opened by fpsom over 4 years ago - 3 comments

#158 - vcfR2genlight failed to convert polyploid of mixed ploidy vcf (obtained by GATK)

Issue - State: open - Opened by lihe-s over 4 years ago - 6 comments

#157 - dplyr 1.0.0 fixes

Pull Request - State: closed - Opened by hadley over 4 years ago - 2 comments

#156 - Compilation failed for package ‘vcfR’

Issue - State: closed - Opened by FannyPouyet over 4 years ago - 3 comments

#155 - issue with as.matrix for subsetting FASTA file to 1 chromosome?

Issue - State: closed - Opened by lesneski over 4 years ago - 7 comments

#154 - dplyr 1.0.0

Issue - State: closed - Opened by knausb over 4 years ago - 1 comment

#153 - VCF files written by `vcfR::write.vcf` not parsed correctly by `bcftools`

Issue - State: closed - Opened by OJWatson over 4 years ago - 4 comments

#152 - Parsing GLnexus pVCF

Issue - State: closed - Opened by ghost over 4 years ago - 10 comments

#151 - Easy way to extract field for plotting?

Issue - State: closed - Opened by ghost over 4 years ago - 2 comments

#150 - class == matrix

Issue - State: closed - Opened by knausb almost 5 years ago - 4 comments

#149 - Update conversion documentation

Pull Request - State: closed - Opened by zkamvar almost 5 years ago - 5 comments

#148 - can I use masker on INFO field values?

Issue - State: closed - Opened by splaisan almost 5 years ago - 3 comments

#147 - Segfault - memory not mapped

Issue - State: closed - Opened by tirohia almost 5 years ago - 3 comments

#146 - Unable to read VCF data

Issue - State: closed - Opened by oalavijeh almost 5 years ago - 3 comments

#145 - changing chromosome ID into numeric or integer

Issue - State: closed - Opened by treebreeder almost 5 years ago - 2 comments

#144 - Missing license version

Issue - State: closed - Opened by jenzopr about 5 years ago - 2 comments

#143 - Support for bcf files

Issue - State: closed - Opened by explodecomputer about 5 years ago - 2 comments

#142 - is.biallelic not working the way you would expect it

Issue - State: closed - Opened by ckastall about 5 years ago - 2 comments

#141 - blank row crashes R - read.vcfR()

Issue - State: open - Opened by TomJamesW about 5 years ago - 4 comments

#140 - Improving run time performance

Issue - State: open - Opened by arumds about 5 years ago - 3 comments

#139 - Error in .shlib_internal(args) : C++11 standard requested but CXX11 is not defined

Issue - State: closed - Opened by tedtoal over 5 years ago - 9 comments

#138 - The following INFO field appears more than once

Issue - State: closed - Opened by tedtoal over 5 years ago - 2 comments

#137 - read.vcfR aborts RStudio/catches segfault in R

Issue - State: closed - Opened by SMartinOSU over 5 years ago - 3 comments

#136 - Create Multisample VCF File

Issue - State: closed - Opened by canholyavkin over 5 years ago - 3 comments

#135 - create.chrom() produces an empty object

Issue - State: closed - Opened by jrhb over 5 years ago - 3 comments

#134 - Can't use a logical vector to subset a vcf when using write.vcf()

Issue - State: closed - Opened by jsstanley over 5 years ago - 2 comments

#133 - R aborted after loading vcf file

Issue - State: closed - Opened by majeedjamakhani over 5 years ago - 4 comments

#132 - Parse CSQ entitities into individual columns

Issue - State: open - Opened by audyavar over 5 years ago - 4 comments

#131 - Missing data not recognized when GT is null but contains more info

Issue - State: closed - Opened by Neato-Nick over 5 years ago - 2 comments

#130 - INFO2df cuts strings with "=" sign

Issue - State: closed - Opened by thedam over 5 years ago - 5 comments

#129 - numeric sample names in read.vcfR

Issue - State: closed - Opened by jessepoland over 5 years ago - 3 comments

#128 - vcfR2genlight() - variation in ploidy determination

Issue - State: open - Opened by fdchevalier over 5 years ago - 5 comments

#127 - vcfR2DNAbin() - no sequence label whith DNAbin list type

Issue - State: open - Opened by fdchevalier over 5 years ago

#126 - vcfR reading problem

Issue - State: closed - Opened by OmidJa over 5 years ago - 3 comments

#125 - Support Tabix

Issue - State: open - Opened by romanzenka over 5 years ago - 9 comments

#124 - VCF files should be block-gzipped and not gzipped

Issue - State: open - Opened by jasper1918 over 5 years ago - 4 comments

#123 - Don't install vcfR in Rstudio make: *** [gt_to_popsum.o] Error 1

Issue - State: closed - Opened by zhenghy over 5 years ago - 1 comment

#122 - vcfR2DNAbin() - problem with DNAbin list type

Issue - State: open - Opened by fdchevalier almost 6 years ago - 2 comments

#121 - extract.haps() does not handle all missing data

Issue - State: open - Opened by fdchevalier almost 6 years ago - 1 comment

#120 - documentation: parameters

Pull Request - State: closed - Opened by Neato-Nick almost 6 years ago - 2 comments

GitHub / knausb/vcfR issues and pull requests