Problem in interpretation of vcf-compare result
variant calling using samtools mpileup
vcf-sort -c, does -c even exist?
vcf-merge error
using VCFtool MAF calculation
vcf-merge missing SNPs in merge
--window-pi Issues
Hi there, I am having a similar issue to the above with the --window-pi setting in...
VCFtools 0.1.15 minDP and maxDP not working
Errors while installing vcftools
The following patch still apllies fine to 0.1.13. Would you mind doing more cleanup?...
Linkage Disequilibrium algorithm
fst for haploid genome
Fst calculation when there is a missing data
Calculation of fst in relation to missing values
Small fix for BCF efficiency
Thank you for calling this to our attention. This patch has been applied to the current...
Fix makefile issue when copying man page when p...
Makefile fails to copy man pages when PREFIX is set
Hi, yes i already realized that the excluded bin have monomorphic SNPs yestarday...
Hi Annarita, For the window-pi function of vcftools, the results from a bin are only...
window-pi vcftools
Argument "." isn't numeric in addition vcf-contrast line 273, <$__ANONIO__> line 859736
Dear David, Thanks for this useful script. I would like to use it but I am having...
Allow user to specify multiple keep and exclude...
Minor edits for C++ 11 compatibility
More cleaning of --LROH function.
Minor change to use (slightly) less memory when...
Minor change to use (slightly) less memory when...
Added --mendel option for finding mendel errors...
Will, I have just committed a new change to the developmental version (v0.1.13) that...
Introduced the --chrom-map option for the --pli...
Drosophila chromosome encoding
Bug fix: The genotype-r2 functions no longer re...
vcf-consensus
Removal of old experimental branches.
Added more specific error cases to the diff fun...
Excellent Anthony, thanks for merging that in so quickly.
Thank you for your help identifying this bug! Your bug fix has now been incorporated...
Error parsing lines with length in multiples of 1024*1024
Bug fix for error parsing gzipped lines with le...
Error parsing lines with length in multiples of 1024*1024
Added warning regarding use of unsorted files i...
*Actually* allow haploid individuals when using...
Improvements to temporary file handling in the ...
Bug fixes for --hap-r2-positions and --geno-r2-...
Bug fix for 'filter sites by mask' function
[Errors installing VCFTools in 32bits ubuntu linux system]
--max-missing yields wrong proportion
Ok, thanks for the clarification. You can close this as invalid. I'll just modify...
The problem here is that your missing data is in the form of a single period '.'...
Here is an example line and the part of the header that is interesting for this situation,...
Here is an example line and the part of the header that is interesting for this situation,...
Here is an example line and the part of the header that is interesting for this situation,...
--max-missing yields wrong proportion
Documentation and website edits
Minor documentation change.
Added 'any' options for filtering by allele cou...
Change to experimental --hapcount function.
Bug fix. Exclude half-genotype calls in Fst cal...
Added experimental --hapcount function.
Tajima's D should be NaN in the absence of data.
Make --hap-r2-positions and --geno-r2-positions...
Minor tidy up of tempfile code in LDhat output ...
Use C++ ofstream for temp files instead of C FI...
Minor changes to LD functions and documentation.
Correction to documentation regarding LD statis...
vcf-to-tab: fix in iupac output
Changes to allow --diff options to output to st...
vcf-subset tries to read dir in the working directory that has the same name as the column given to the -c option
Edits to documentation and website for new patch
Edited the diff switch error function to provid...
This patch fixes the issue: --- vcf-consensus 2014-03-26 15:40:25.000000000 +0000...
Fixed a segfault bug in the plink and plink tpe...
The --diff option now also includes an 'overlap...
Added --indv-burden option.
Added functions --positions-overlap and --exclu...
Edits to the LD functions so they use less spac...
Allow different handling of hom-alt variants in...
Stop segfault for --indv-freq-burden when encou...
Overhaul for vcftools diff functions
Added option --temp to allow users to choose a ...
Multiple bed files may no longer be used togeth...
Bug fix for the Long Run of Homozygosity function
Use scientific notation for --hardy p-values.
Added tests for too many / too few heterozygote...
Don't count SVs when making indel length histog...
Be a bit more strict when filtering indels (i.e...
vcf-consensus misinterprets <DEL> allele
Allow mismatch of ALT and REF bases for vcf-merge
Edits to vcftools man page and website document...
Fix to --indv-freq-burden.
Added --indv-freq-burden as an experimental fun...