Activity for vcftools

Priyanka created ticket #29

Priyanka — Thu, 07 May 2020 05:58:08 -0000

Problem in interpretation of vcf-compare result

Malena Serrano created ticket #67

Malena Serrano — Tue, 14 May 2019 09:11:49 -0000

variant calling using samtools mpileup

Sky Scraper created ticket #66

Sky Scraper — Fri, 29 Mar 2019 04:53:31 -0000

vcf-sort -c, does -c even exist?

Anna Nash created ticket #65

Anna Nash — Mon, 08 Oct 2018 12:21:27 -0000

vcf-merge error

Sudhir S Jadhao created ticket #64

Sudhir S Jadhao — Wed, 12 Sep 2018 04:45:11 -0000

using VCFtool MAF calculation

Anna Nash created ticket #63

Anna Nash — Mon, 08 Jan 2018 16:43:43 -0000

vcf-merge missing SNPs in merge

John Mattick created ticket #62

John Mattick — Mon, 03 Apr 2017 18:33:23 -0000

--window-pi Issues

John Mattick posted a comment on ticket #57

John Mattick — Wed, 29 Mar 2017 17:36:32 -0000

Hi there, I am having a similar issue to the above with the --window-pi setting in...

Marc-Olivier Beausoleil created ticket #61

Marc-Olivier Beausoleil — Sat, 26 Nov 2016 14:48:50 -0000

VCFtools 0.1.15 minDP and maxDP not working

Prathyusha Konda created ticket #60

Prathyusha Konda — Fri, 23 Sep 2016 18:23:41 -0000

Errors while installing vcftools

Martin Mokrejs posted a comment on ticket #58

Martin Mokrejs — Sun, 31 Jul 2016 20:22:07 -0000

The following patch still apllies fine to 0.1.13. Would you mind doing more cleanup?...

Jhon created ticket #28

Jhon — Thu, 21 Apr 2016 15:35:47 -0000

Linkage Disequilibrium algorithm

prakash kancherla created ticket #27

prakash kancherla — Mon, 15 Feb 2016 13:58:52 -0000

fst for haploid genome

Lau created ticket #59

Lau — Sat, 21 Nov 2015 17:28:02 -0000

Fst calculation when there is a missing data

Lau created ticket #26

Lau — Fri, 20 Nov 2015 21:04:50 -0000

Calculation of fst in relation to missing values

vcftools released /README.txt

vcftools — Mon, 03 Aug 2015 13:46:02 -0000

vcftools released /vcftools_0.1.13.tar.gz

vcftools — Mon, 03 Aug 2015 13:46:02 -0000

Anthony Marcketta committed [r1005]

Anthony Marcketta — Tue, 07 Jul 2015 19:55:47 -0000

Small fix for BCF efficiency

Anthony Marcketta posted a comment on ticket #58

Anthony Marcketta — Wed, 24 Jun 2015 15:04:37 -0000

Thank you for calling this to our attention. This patch has been applied to the current...

Anthony Marcketta committed [r1004]

Anthony Marcketta — Wed, 24 Jun 2015 15:03:51 -0000

Fix makefile issue when copying man page when p...

Carl Thomas created ticket #58

Carl Thomas — Wed, 24 Jun 2015 05:04:45 -0000

Makefile fails to copy man pages when PREFIX is set

annarita posted a comment on ticket #57

annarita — Wed, 10 Jun 2015 19:18:30 -0000

Hi, yes i already realized that the excluded bin have monomorphic SNPs yestarday...

Anthony Marcketta posted a comment on ticket #57

Anthony Marcketta — Wed, 10 Jun 2015 18:06:39 -0000

Hi Annarita, For the window-pi function of vcftools, the results from a bin are only...

annarita created ticket #57

annarita — Tue, 09 Jun 2015 20:10:54 -0000

window-pi vcftools

alig created ticket #56

alig — Mon, 25 May 2015 07:56:03 -0000

Argument "." isn't numeric in addition vcf-contrast line 273, <$__ANONIO__> line 859736

Gabriel posted a comment on ticket #19

Gabriel — Mon, 04 May 2015 16:36:23 -0000

Dear David, Thanks for this useful script. I would like to use it but I am having...

Anthony Marcketta committed [r1003]

Anthony Marcketta — Fri, 01 May 2015 13:54:54 -0000

Allow user to specify multiple keep and exclude...

Anthony Marcketta committed [r1002]

Anthony Marcketta — Tue, 14 Apr 2015 15:00:34 -0000

Minor edits for C++ 11 compatibility

Adam Auton committed [r1001]

Adam Auton — Thu, 09 Apr 2015 17:18:26 -0000

More cleaning of --LROH function.

Adam Auton committed [r1000]

Adam Auton — Wed, 08 Apr 2015 19:59:09 -0000

Minor change to use (slightly) less memory when...

Adam Auton committed [r999]

Adam Auton — Wed, 08 Apr 2015 19:13:54 -0000

Minor change to use (slightly) less memory when...

Adam Auton committed [r998]

Adam Auton — Wed, 08 Apr 2015 18:35:43 -0000

Added --mendel option for finding mendel errors...

Anthony Marcketta posted a comment on ticket #25

Anthony Marcketta — Tue, 07 Apr 2015 18:51:41 -0000

Will, I have just committed a new change to the developmental version (v0.1.13) that...

Anthony Marcketta committed [r997]

Anthony Marcketta — Tue, 07 Apr 2015 18:27:35 -0000

Introduced the --chrom-map option for the --pli...

William Gilks created ticket #25

William Gilks — Mon, 06 Apr 2015 21:57:29 -0000

Drosophila chromosome encoding

Anthony Marcketta committed [r996]

Anthony Marcketta — Tue, 10 Mar 2015 17:14:27 -0000

Bug fix: The genotype-r2 functions no longer re...

Yun Heo created ticket #54

Yun Heo — Sat, 14 Feb 2015 06:16:49 -0000

vcf-consensus

Adam Auton committed [r995]

Adam Auton — Fri, 13 Feb 2015 19:51:49 -0000

Removal of old experimental branches.

Anthony Marcketta committed [r994]

Anthony Marcketta — Thu, 29 Jan 2015 20:49:07 -0000

Added more specific error cases to the diff fun...

ThomasJ posted a comment on ticket #53

ThomasJ — Wed, 28 Jan 2015 19:49:28 -0000

Excellent Anthony, thanks for merging that in so quickly.

Anthony Marcketta posted a comment on ticket #53

Anthony Marcketta — Wed, 28 Jan 2015 17:50:16 -0000

Thank you for your help identifying this bug! Your bug fix has now been incorporated...

Anthony Marcketta modified ticket #53

Anthony Marcketta — Wed, 28 Jan 2015 17:50:16 -0000

Error parsing lines with length in multiples of 1024*1024

Anthony Marcketta committed [r993]

Anthony Marcketta — Wed, 28 Jan 2015 17:48:34 -0000

Bug fix for error parsing gzipped lines with le...

ThomasJ created ticket #53

ThomasJ — Mon, 26 Jan 2015 20:31:12 -0000

Error parsing lines with length in multiples of 1024*1024

Anthony Marcketta committed [r992]

Anthony Marcketta — Tue, 13 Jan 2015 20:32:43 -0000

Added warning regarding use of unsorted files i...

Adam Auton committed [r991]

Adam Auton — Fri, 09 Jan 2015 14:25:52 -0000

*Actually* allow haploid individuals when using...

Anthony Marcketta committed [r990]

Anthony Marcketta — Thu, 11 Dec 2014 15:57:00 -0000

Improvements to temporary file handling in the ...

Anthony Marcketta committed [r989]

Anthony Marcketta — Tue, 09 Dec 2014 19:48:15 -0000

Bug fixes for --hap-r2-positions and --geno-r2-...

Anthony Marcketta committed [r988]

Anthony Marcketta — Mon, 08 Dec 2014 19:56:52 -0000

Bug fix for 'filter sites by mask' function

Jaume Sastre created ticket #52

Jaume Sastre — Sat, 06 Dec 2014 17:01:05 -0000

[Errors installing VCFTools in 32bits ubuntu linux system]

Adam Auton modified ticket #51

Adam Auton — Thu, 04 Dec 2014 14:26:16 -0000

--max-missing yields wrong proportion

Francisco Pina Martins posted a comment on ticket #51

Francisco Pina Martins — Wed, 03 Dec 2014 17:26:55 -0000

Ok, thanks for the clarification. You can close this as invalid. I'll just modify...

Anthony Marcketta posted a comment on ticket #51

Anthony Marcketta — Wed, 03 Dec 2014 16:40:46 -0000

The problem here is that your missing data is in the form of a single period '.'...

Francisco Pina Martins modified a comment on ticket #51

Francisco Pina Martins — Wed, 03 Dec 2014 11:00:57 -0000

Here is an example line and the part of the header that is interesting for this situation,...

Francisco Pina Martins modified a comment on ticket #51

Francisco Pina Martins — Wed, 03 Dec 2014 11:00:28 -0000

Here is an example line and the part of the header that is interesting for this situation,...

Francisco Pina Martins posted a comment on ticket #51

Francisco Pina Martins — Wed, 03 Dec 2014 10:58:18 -0000

Here is an example line and the part of the header that is interesting for this situation,...

Francisco Pina Martins created ticket #51

Francisco Pina Martins — Tue, 02 Dec 2014 14:29:42 -0000

--max-missing yields wrong proportion

Anthony Marcketta committed [r987]

Anthony Marcketta — Tue, 11 Nov 2014 20:24:29 -0000

Documentation and website edits

Adam Auton committed [r986]

Adam Auton — Mon, 10 Nov 2014 16:03:55 -0000

Minor documentation change.

Adam Auton committed [r985]

Adam Auton — Mon, 10 Nov 2014 15:58:01 -0000

Added 'any' options for filtering by allele cou...

Adam Auton committed [r984]

Adam Auton — Thu, 30 Oct 2014 19:07:54 -0000

Change to experimental --hapcount function.

Adam Auton committed [r983]

Adam Auton — Thu, 25 Sep 2014 19:11:29 -0000

Bug fix. Exclude half-genotype calls in Fst cal...

Adam Auton committed [r982]

Adam Auton — Thu, 25 Sep 2014 17:45:34 -0000

Added experimental --hapcount function.

Adam Auton committed [r981]

Adam Auton — Tue, 23 Sep 2014 20:43:56 -0000

Tajima's D should be NaN in the absence of data.

Adam Auton committed [r980]

Adam Auton — Mon, 08 Sep 2014 00:33:10 -0000

Make --hap-r2-positions and --geno-r2-positions...

Adam Auton committed [r979]

Adam Auton — Thu, 04 Sep 2014 16:39:56 -0000

Minor tidy up of tempfile code in LDhat output ...

Adam Auton committed [r978]

Adam Auton — Wed, 03 Sep 2014 18:43:59 -0000

Use C++ ofstream for temp files instead of C FI...

Adam Auton committed [r977]

Adam Auton — Wed, 03 Sep 2014 13:43:14 -0000

Minor changes to LD functions and documentation.

Adam Auton committed [r976]

Adam Auton — Tue, 02 Sep 2014 14:31:37 -0000

Correction to documentation regarding LD statis...

Petr Danecek committed [r975]

Petr Danecek — Thu, 28 Aug 2014 07:22:01 -0000

vcf-to-tab: fix in iupac output

Adam Auton committed [r974]

Adam Auton — Wed, 27 Aug 2014 19:25:33 -0000

Changes to allow --diff options to output to st...

David Blaney created ticket #50

David Blaney — Tue, 05 Aug 2014 13:50:18 -0000

vcf-subset tries to read dir in the working directory that has the same name as the column given to the -c option

vcftools released /vcftools_0.1.12b.tar.gz

vcftools — Mon, 04 Aug 2014 17:42:03 -0000

Anthony Marcketta committed [r973]

Anthony Marcketta — Fri, 01 Aug 2014 19:08:42 -0000

Edits to documentation and website for new patch

Anthony Marcketta committed [r972]

Anthony Marcketta — Tue, 29 Jul 2014 19:14:51 -0000

Edited the diff switch error function to provid...

Javier Herrero posted a comment on ticket #49

Javier Herrero — Tue, 29 Jul 2014 11:29:07 -0000

This patch fixes the issue: --- vcf-consensus 2014-03-26 15:40:25.000000000 +0000...

Anthony Marcketta committed [r971]

Anthony Marcketta — Fri, 25 Jul 2014 17:59:57 -0000

Fixed a segfault bug in the plink and plink tpe...

Anthony Marcketta committed [r970]

Anthony Marcketta — Fri, 18 Jul 2014 17:47:11 -0000

The --diff option now also includes an 'overlap...

Adam Auton committed [r969]

Adam Auton — Thu, 17 Jul 2014 17:48:37 -0000

Added --indv-burden option.

Anthony Marcketta committed [r968]

Anthony Marcketta — Thu, 17 Jul 2014 14:29:39 -0000

Added functions --positions-overlap and --exclu...

Anthony Marcketta committed [r967]

Anthony Marcketta — Wed, 16 Jul 2014 19:26:39 -0000

Edits to the LD functions so they use less spac...

Adam Auton committed [r966]

Adam Auton — Fri, 11 Jul 2014 18:16:50 -0000

Allow different handling of hom-alt variants in...

Adam Auton committed [r965]

Adam Auton — Tue, 08 Jul 2014 15:19:18 -0000

Stop segfault for --indv-freq-burden when encou...

Anthony Marcketta committed [r964]

Anthony Marcketta — Wed, 02 Jul 2014 20:15:00 -0000

Overhaul for vcftools diff functions

Anthony Marcketta committed [r963]

Anthony Marcketta — Wed, 25 Jun 2014 19:59:51 -0000

Added option --temp to allow users to choose a ...

Anthony Marcketta committed [r962]

Anthony Marcketta — Tue, 24 Jun 2014 16:13:56 -0000

Multiple bed files may no longer be used togeth...

Anthony Marcketta committed [r961]

Anthony Marcketta — Mon, 23 Jun 2014 19:50:46 -0000

Bug fix for the Long Run of Homozygosity function

Adam Auton committed [r960]

Adam Auton — Thu, 19 Jun 2014 14:56:43 -0000

Use scientific notation for --hardy p-values.

Adam Auton committed [r959]

Adam Auton — Thu, 19 Jun 2014 14:16:18 -0000

Added tests for too many / too few heterozygote...

Adam Auton committed [r958]

Adam Auton — Tue, 17 Jun 2014 17:17:48 -0000

Don't count SVs when making indel length histog...

Adam Auton committed [r957]

Adam Auton — Mon, 16 Jun 2014 16:05:56 -0000

Be a bit more strict when filtering indels (i.e...

Javier Herrero created ticket #49

Javier Herrero — Mon, 09 Jun 2014 13:43:23 -0000

vcf-consensus misinterprets ~~allele~~

Thon de Boer created ticket #24

Thon de Boer — Wed, 28 May 2014 23:12:18 -0000

Allow mismatch of ALT and REF bases for vcf-merge

Anthony Marcketta committed [r956]

Anthony Marcketta — Fri, 23 May 2014 20:35:00 -0000

Edits to vcftools man page and website document...

Adam Auton committed [r955]

Adam Auton — Wed, 21 May 2014 20:24:02 -0000

Fix to --indv-freq-burden.

Adam Auton committed [r954]

Adam Auton — Wed, 21 May 2014 17:57:55 -0000

Added --indv-freq-burden as an experimental fun...