Activity for vcftools
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Priyanka created ticket #29
Problem in interpretation of vcf-compare result
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Malena Serrano created ticket #67
variant calling using samtools mpileup
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Sky Scraper created ticket #66
vcf-sort -c, does -c even exist?
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Anna Nash created ticket #65
vcf-merge error
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Sudhir S Jadhao created ticket #64
using VCFtool MAF calculation
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vcf-merge missing SNPs in merge
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John Mattick created ticket #62
--window-pi Issues
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Hi there, I am having a similar issue to the above with the --window-pi setting in...
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Marc-Olivier Beausoleil created ticket #61
VCFtools 0.1.15 minDP and maxDP not working
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Prathyusha Konda created ticket #60
Errors while installing vcftools
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Martin Mokrejs posted a comment on ticket #58
The following patch still apllies fine to 0.1.13. Would you mind doing more cleanup?...
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Jhon created ticket #28
Linkage Disequilibrium algorithm
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prakash kancherla created ticket #27
fst for haploid genome
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Lau created ticket #59
Fst calculation when there is a missing data
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Calculation of fst in relation to missing values
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vcftools released /README.txt
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Anthony Marcketta committed [r1005]
Small fix for BCF efficiency
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Thank you for calling this to our attention. This patch has been applied to the current...
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Fix makefile issue when copying man page when p...
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Carl Thomas created ticket #58
Makefile fails to copy man pages when PREFIX is set
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annarita posted a comment on ticket #57
Hi, yes i already realized that the excluded bin have monomorphic SNPs yestarday...
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Hi Annarita, For the window-pi function of vcftools, the results from a bin are only...
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window-pi vcftools
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alig created ticket #56
Argument "." isn't numeric in addition vcf-contrast line 273, <$__ANONIO__> line 859736
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Gabriel posted a comment on ticket #19
Dear David, Thanks for this useful script. I would like to use it but I am having...
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Allow user to specify multiple keep and exclude...
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Minor edits for C++ 11 compatibility
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Adam Auton committed [r1001]
More cleaning of --LROH function.
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Minor change to use (slightly) less memory when...
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Minor change to use (slightly) less memory when...
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Added --mendel option for finding mendel errors...
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Will, I have just committed a new change to the developmental version (v0.1.13) that...
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Introduced the --chrom-map option for the --pli...
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William Gilks created ticket #25
Drosophila chromosome encoding
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Bug fix: The genotype-r2 functions no longer re...
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Yun Heo created ticket #54
vcf-consensus
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Removal of old experimental branches.
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Added more specific error cases to the diff fun...
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ThomasJ posted a comment on ticket #53
Excellent Anthony, thanks for merging that in so quickly.
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Thank you for your help identifying this bug! Your bug fix has now been incorporated...
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Error parsing lines with length in multiples of 1024*1024
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Bug fix for error parsing gzipped lines with le...
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Error parsing lines with length in multiples of 1024*1024
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Added warning regarding use of unsorted files i...
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*Actually* allow haploid individuals when using...
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Improvements to temporary file handling in the ...
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Bug fixes for --hap-r2-positions and --geno-r2-...
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Bug fix for 'filter sites by mask' function
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Jaume Sastre created ticket #52
[Errors installing VCFTools in 32bits ubuntu linux system]
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--max-missing yields wrong proportion
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Francisco Pina Martins posted a comment on ticket #51
Ok, thanks for the clarification. You can close this as invalid. I'll just modify...
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The problem here is that your missing data is in the form of a single period '.'...
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Here is an example line and the part of the header that is interesting for this situation,...
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Here is an example line and the part of the header that is interesting for this situation,...
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Here is an example line and the part of the header that is interesting for this situation,...
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--max-missing yields wrong proportion
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Documentation and website edits
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Minor documentation change.
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Added 'any' options for filtering by allele cou...
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Change to experimental --hapcount function.
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Bug fix. Exclude half-genotype calls in Fst cal...
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Added experimental --hapcount function.
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Tajima's D should be NaN in the absence of data.
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Make --hap-r2-positions and --geno-r2-positions...
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Minor tidy up of tempfile code in LDhat output ...
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Use C++ ofstream for temp files instead of C FI...
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Minor changes to LD functions and documentation.
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Correction to documentation regarding LD statis...
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Petr Danecek committed [r975]
vcf-to-tab: fix in iupac output
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Changes to allow --diff options to output to st...
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David Blaney created ticket #50
vcf-subset tries to read dir in the working directory that has the same name as the column given to the -c option
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Edits to documentation and website for new patch
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Edited the diff switch error function to provid...
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Javier Herrero posted a comment on ticket #49
This patch fixes the issue: --- vcf-consensus 2014-03-26 15:40:25.000000000 +0000...
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Fixed a segfault bug in the plink and plink tpe...
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The --diff option now also includes an 'overlap...
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Added --indv-burden option.
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Added functions --positions-overlap and --exclu...
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Edits to the LD functions so they use less spac...
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Allow different handling of hom-alt variants in...
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Stop segfault for --indv-freq-burden when encou...
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Overhaul for vcftools diff functions
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Added option --temp to allow users to choose a ...
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Multiple bed files may no longer be used togeth...
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Bug fix for the Long Run of Homozygosity function
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Use scientific notation for --hardy p-values.
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Added tests for too many / too few heterozygote...
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Don't count SVs when making indel length histog...
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Be a bit more strict when filtering indels (i.e...
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vcf-consensus misinterprets <DEL> allele
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Thon de Boer created ticket #24
Allow mismatch of ALT and REF bases for vcf-merge
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Edits to vcftools man page and website document...
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Fix to --indv-freq-burden.
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Added --indv-freq-burden as an experimental fun...