knausb vcfR issues - Githubissues

knausb / vcfR

Tools to work with variant call format files

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issues

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

#214 gevro opened 2 months ago
12
See sequence length

#213 jenifferteles opened 8 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 2 years ago
2
gene/chromosome annotation

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

#201 gorgitko closed 2 years ago
6
vcfR2tidy can't handle files with empty INFO

#200 alkaZeltser opened 2 years ago
4
Rename Genotype information

#199 Flavjack closed 2 years 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 3 years ago
6
How to avoid to print the vcfR header?

#191 Shicheng-Guo opened 3 years ago
2
0 percent missing data

#190 redgcko7 closed 3 years ago
2
vcfr, extract.gt, bcftools, vcf format incompatible?

#189 wbsimey closed 3 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 4 years ago
1
Read depth can not be plotted from VCF file

#173 AG-Run closed 4 years ago
1
Error in extract.gt(vcf) - ID column contains non-unique names

#172 gimeno99 closed 4 years ago
2
Put gt back to vcf

#171 zoeluo15 closed 4 years ago
2
vcfR: ID column contains non-unique names

#170 gimeno99 closed 4 years ago
7
not available for R4.0

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

#168 brockels closed 4 years ago
3
s3read_using lasts forever reading a VCF file

#167 HediaTnani closed 4 years ago
1
read.vcfR randomly dropping genotypes

#166 akijarl closed 4 years ago
2
CRAN not supporting vcfR

#165 jonathan-velotta closed 4 years ago
9