knausb vcfR issues - Githubissues

knausb / vcfR

Tools to work with variant call format files

239 stars 54 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

See sequence length

#213 jenifferteles opened 3 months ago
1
change genotype(change gap to NA)

#212 snackens closed 1 year ago
2
vcfR Subsetting to the first chromosome

#211 charbel2998 opened 1 year ago
1
Hide a panel from chromoqc or plot

#210 NowickiLab closed 1 year ago
2
compilation issue

#209 knausb closed 1 year ago
2
extract.gt() missing heterozygotes

#208 samarth8392 opened 1 year ago
1
read.vcfR() not recognizing missing data

#207 loukiaspi closed 1 year ago
3
chromR object not finding DP and MQ values

#206 JuanitaGil closed 1 year ago
2
Assign_Indiv_by_Geno.R function of Demuxafy.sif problems with the vcf

#205 ElenaSLuis opened 1 year ago
1
Filtering for minor allele Frequency

#204 mattbareno closed 1 year ago
4
write.vcf() not filtering variants

#203 mattbareno closed 1 year ago
2
gene/chromosome annotation

#202 umasstr closed 1 year ago
2
new feature: separation of annotation columns in tidy dataframes from VCFs annotated by snpEff or VEP tools

#201 gorgitko closed 1 year ago
6
vcfR2tidy can't handle files with empty INFO

#200 alkaZeltser opened 1 year ago
4
Rename Genotype information

#199 Flavjack closed 1 year ago
2
read.vcfR() coredump with empty lines in input

#198 ntakebay opened 2 years ago
5
Heterozygous SNP calling

#197 ettorefedele closed 2 years ago
15
vcfR not recognizing all chromosomes

#196 lukaskon closed 2 years ago
2
RStudio Session aborted when writing VCF

#195 eibol1 closed 2 years ago
0
How can I add population information to genind converted using vcfR2genind?

#194 kopelol closed 2 years ago
2
Error: ID column contains non-unique names

#193 bathycy opened 2 years ago
1
Variants with MAF of 0 after removing monomorphics

#192 Neato-Nick closed 2 years ago
6
How to avoid to print the vcfR header?

#191 Shicheng-Guo opened 2 years ago
2
0 percent missing data

#190 redgcko7 closed 2 years ago
2
vcfr, extract.gt, bcftools, vcf format incompatible?

#189 wbsimey closed 2 years ago
6
does it support vcf comes from vep or vardict

#188 worker000000 opened 3 years ago
1
Combine Two Variants In One Single VCF File

#187 gk7279 closed 3 years ago
2
Unable to convert to long-format using vcfR2tidy

#186 oisinmccaffrey closed 3 years ago
0
Understanding genetic_diff() number of alleles output

#185 EveTC opened 3 years ago
4
error while accessing filltered vcf file

#184 sekhwal closed 3 years ago
1
About vcfR::heatmap.bp, is there a way to scale the heatmap but keep the barplot as sum of unscaled values?

#183 hope-data-science opened 3 years ago
2
sex determination

#182 AnjaliC4 opened 3 years ago
8
Convert vcfR object to tabular format

#181 Al-Murphy closed 3 years ago
3
Adding INFO tags on the basis information in the INFO tags

#180 misrak closed 3 years ago
4
Subset or downsample a VCF file?

#179 vertesy closed 3 years ago
2
is.polymorphic bug, returns FALSE for a sample of all hets?

#178 JimWhiting91 closed 3 years ago
9
How to work with multiple vcf files?

#177 zh-zhang1984 closed 3 years ago
2
overlapping sliding window

#176 michaeljmetzger opened 3 years ago
2
After using read.vcfR file format is not recognised * This is not a vcf!

#175 frederikvand closed 3 years ago
0
vcfR reading INFO/DS field

#174 meixilin opened 3 years ago
1
Read depth can not be plotted from VCF file

#173 AG-Run closed 3 years ago
1
Error in extract.gt(vcf) - ID column contains non-unique names

#172 gimeno99 closed 3 years ago
2
Put gt back to vcf

#171 zoeluo15 closed 3 years ago
2
vcfR: ID column contains non-unique names

#170 gimeno99 closed 3 years ago
7
not available for R4.0

#169 complexgenome closed 3 years ago
4
cannot install for R version 4 on Mac

#168 brockels closed 3 years ago
3
s3read_using lasts forever reading a VCF file

#167 HediaTnani closed 3 years ago
1
read.vcfR randomly dropping genotypes

#166 akijarl closed 3 years ago
2
CRAN not supporting vcfR

#165 jonathan-velotta closed 3 years ago
9
Addresses issue CHROM param in create.chromR #52

#164 RichardJActon opened 4 years ago
1