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From: Adam A. <ada...@gm...> - 2015-07-21 23:33:12
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Dear all, I'm pleased to announce the VCFtools is moving to GitHub! The new website can be found here: https://vcftools.github.io/ At the same time, we're also announcing the release of version v0.1.13, which includes a number of optimizations and bug fixes. A description of the changes can be found at the end of this email. All users are encouraged to upgrade as soon as possible. We were going to announce this move a little later, but as SourceForge has been down for a few days, we decided to make the announcement earlier. If you discover any problems working with the new GitHub site, please do let us know. When the old SourceForge site returns, we will complete the relocation. Thank you, and kind regards, Adam -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Center, Room 353B, Bronx, New York 10461 Tel: +1 (718) 678 1150 vcftools v0.1.13 release notes - Migration of the vcftools project (and website) from sourceforge to github - Optimizations for reading and writing BCF files - Edits to code for C++ 11 compatibility - Added --mendel option for finding Mendelian errors in trios - Allow --diff options to output to stream by splitting up function into --diff-site and --diff-indv options - Added experimental --hapcount function to determine the amount of unique haplotypes in user defined bins - Addition of "any" options to filter by frequency or count of any alternate allele (instead of requiring all of them to pass) - Improvements to temporary file handling for all LD functions - Added --chrom-map option to allow user specified chromosomes for writing out plink files - Allow site filtering with multiple keep and exclude files - Tajima's D now reports NaN in the absence of data - Various bug fixes |
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From: Anthony M. <ant...@ei...> - 2014-08-04 17:48:00
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Dear vcftools users, We have just released a new patch for vcftools. The new version is available through the SVN repository or from the sourceforge website. https://sourceforge.net/projects/vcftools/ Many of the changes for this patch are bug fixes and 'under the hood' improvements including the following: - Diff functions no longer write to temporary files, but instead scan through both files simultaneously. Files must be sorted in the same chromosomal order. - All linkage disequilibrium functions now write fewer and smaller temporary files. - Added an option to allow user to specify the location of temporary files. - Regular diff function now reports if a site from one file overlaps with a site from the other file. - Switch error diff function now reports a range of bases where the switch may have occurred. - Bug fix for long run of homozygosity function. - Added filters --positions-overlap and --exclude-positions-overlap to filter out any sites that overlap any positions in a given file. - Added the --contigs parameter for declaring contigs not found in the header for vcf to bcf conversion. Thank you, Anthony -- Anthony Marcketta Bioinformatics Analyst Department of Genetics Albert Einstein College of Medicine Price Center 353D Bronx, New York 10461 |
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From: Adam A. <ada...@gm...> - 2014-03-26 17:38:40
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Dear all, We have just released a minor update to VCFtools, which fixes a newly introduced bug that occured when using the --fst-window-size option. The new version is available via the SVN or from the sourceforge website: https://sourceforge.net/projects/vcftools/ Thank you, Adam -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Van Etten B06, Bronx, New York 10461 Tel: +1 (718) 839 7216 |
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From: Adam A. <ada...@gm...> - 2014-03-06 16:15:37
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Dear VCFtools users, I'm pleased to announce the release of VCFtools v0.1.12, which was posted as a tarball a few minutes ago. This version can be downloaded from here: http://sourceforge.net/projects/vcftools/files/ Version v0.1.12 represents a fairly major revision, and includes a number of important changes and bug fixes. All users are encouraged to update as soon as possible. Importantly, *this version includes support for working on standard input and output streams*, which dramatically improves the programs flexibility. For usage examples please visit this page: http://vcftools.sourceforge.net/documentation.html A list of changes follows this email. Thank you, Adam Added options: --stdout, -c : These options force the program to write to standard out instead of directly to file --relatedness2 : Calculate and output a relatedness statistic based on the method of Manichaikul et al., Bioinformatics 2010 Removed options: --min-indv-meanDP <float> --max-indv-mean-DP <float> --mind <float> --recode-to-stream (functionality replaced by --recode used with --stdout) --recode-bcf-to-stream (functionality replaced by --recode-bcf used with --stdout) --force-write-index Changed options: --vcf, --gzvcf, --bcf : These options now can accept a dash character "-" instead of a filename, allowing the program to read from standard input. --phased : Now this function only removes sites with unphased genotypes and does not remove individuals with all unphased genotypes. --missing : This function has been split into two separate functions that provides the same functionality as the previously: --missing-indv and --missing-site --filtered-sites : This function has been split into two separate functions that provides the same functionality as the previously: --kept-sites and --removed-sites --TsTv <int> : This function no longer outputs a summary along with the TsTv bin file. To output only the summary file, use function: --TsTv-summary --geno <float> : This option has been renamed --max-missing <float> but keeps the same functionality. -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Van Etten B06, Bronx, New York 10461 Tel: +1 (718) 839 7216 |
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From: Adam A. <ada...@gm...> - 2013-09-19 19:43:36
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Dear all, In the past few weeks, we have been busily working on a new version of vcftools that supports working on streams. This should enable the use of vcftools within various pipelines without the need of writing to disk, and hopefully will be useful to a number of people. To implement this feature, we've had to substantially revise the internal workings of vcftools. As such, we're releasing it as an experimental version in the hope that people will help us test the program and identify bugs before we make a "formal" release. The new version can be obtained from a branch of the SVN: - svn checkout svn://svn.code.sf.net/p/vcftools/code/branches/streamvcftools_stream Below are a number of examples of the type of functionality one can achieve with this new version: Standard functionality - vcftools --vcf sample.vcf --freq --out sample_output Input stream functionality - cat sample.vcf | vcftools --vcf --het --out sample_output - zcat sample.vcf.gz | vcftools --gzvcf --het --out sample_output Output stream functionality - cat sample.vcf | vcftools --vcf --freq --stdout > sample_output.frq BCF to gzipped VCF conversion functionality - vcftools --bcf sample.bcf --recode --recode-INFO-all --stdout | bgzip -c > sample.vcf.gz Using both standard out and standard error - vcftools --vcf sample.vcf --hardy > sample.hardy.output 2> sample.log In addition, because of some of the changes to the internal workings of vcftools, a number of previously available options have either been removed, or now function slightly differently. Removed: - --min-indv-meanDP <float> - --max-indv-mean-DP <float> - --mind <float> - --recode-to-stream - --recode-bcf-to-stream - --force-write-index Changed options: - --phased : Now this function only removes sites with unphased genotypes and does not remove individuals with all unphased genotypes. - --missing : This function no longer exists, it has been split into two separate functions that provides the same functionality as the previous one: --missing-indv and --missing-site - --filtered-sites : This function no longer exists, it has been split into two separate functions that provides the same functionality as the previous one: --kept-sites and --removed-sites - --TsTv <int> : This function no longer outputs a summary along with the TsTv bin file. To output only the summary file, use function: --TsTv-summary Please do give the new version a try and let us know of us any issues you find. I'd like to emphasize that this version is still quite experimental, so please also be patient as we work our way through the various issues. Many thanks, Adam -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Van Etten B06, Bronx, New York 10461 Tel: +1 (718) 839 7216 |
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From: Adam A. <ada...@gm...> - 2013-06-13 15:03:41
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Dear VCFtools users, I'm pleased to announce the release of VCFtools v0.1.11, which was posted as a tarball a few minutes ago. This version can be downloaded from here: http://sourceforge.net/projects/vcftools/ Version v0.1.11 includes a number of important changes and bug fixes, and all users are encouraged to update as soon as possible. Highlights include preliminary support for the BCFv2 format within vcftools, which can be substantially quicker when working with larger files. Also, the licence has been changed to GNU Lesser General Public License version 3.0 (LGPLv3). A full change list follows this email. Kind regards, Adam Auton r865 | auton1 | 2013-06-13 10:40:16 EDT Updated version number in preparation for new release. Cleaned a few things to fix compiler warnings. ---------------------------------------------------------------------------- r864 | amarcket | 2013-06-11 13:57:32 EDT Fix in BED file filtering in the case of multiple alternate alleles ---------------------------------------------------------------------------- r863 | petulda | 2013-06-11 04:38:48 EDT Added --haplotype option ---------------------------------------------------------------------------- r862 | auton1 | 2013-06-06 15:56:25 EDT Allow mapping between individuals when using --diff (--diff-indv-map). ---------------------------------------------------------------------------- r861 | auton1 | 2013-06-04 14:20:17 EDT Allow positions file to be gzipped (--exclude-positions). ---------------------------------------------------------------------------- r860 | auton1 | 2013-06-04 13:53:58 EDT Allow positions file to be gzipped (--positions). ---------------------------------------------------------------------------- r859 | auton1 | 2013-05-31 10:10:25 EDT Check VCF is sorted when writing index. ---------------------------------------------------------------------------- r858 | auton1 | 2013-05-31 10:04:55 EDT Check VCF is sorted when writing index. ---------------------------------------------------------------------------- r857 | petulda | 2013-05-28 07:09:13 EDT Sanity check for conflicting variants, resolve by skipping ---------------------------------------------------------------------------- r856 | auton1 | 2013-05-24 16:41:42 EDT Restored --remove-indel functionality lost during BCF revisions. ---------------------------------------------------------------------------- r855 | auton1 | 2013-05-17 16:50:20 EDT Added --geno-chisq to allow calculation of LD with multiple alleles. ---------------------------------------------------------------------------- r854 | amarcket | 2013-05-14 14:50:18 EDT Fixed parsing of CONTIG header lines ---------------------------------------------------------------------------- r853 | auton1 | 2013-05-14 11:30:49 EDT Fix to handle ploidy when there is no GT field. ---------------------------------------------------------------------------- r852 | auton1 | 2013-05-14 10:07:06 EDT Fix to output correct values of D in --hap-r2. ---------------------------------------------------------------------------- r851 | petulda | 2013-05-14 09:52:43 EDT Another minor update in web docs ---------------------------------------------------------------------------- r850 | petulda | 2013-05-14 09:41:31 EDT Updated documentation ---------------------------------------------------------------------------- r849 | amarcket | 2013-05-08 11:14:57 EDT Further clarification of the vcftools options that filter sites based on filter tags ---------------------------------------------------------------------------- r848 | amarcket | 2013-05-02 10:10:57 EDT A minor fix for the PCA function ---------------------------------------------------------------------------- r847 | amarcket | 2013-05-02 09:44:15 EDT Small correction for mistake made in BCF adaptation ---------------------------------------------------------------------------- r846 | amarcket | 2013-05-01 16:44:07 EDT Major alteration of code for BCF compatibility ---------------------------------------------------------------------------- r845 | auton1 | 2013-04-30 15:00:52 EDT Minor fix to filtering by non-ref allele freq. ---------------------------------------------------------------------------- r844 | auton1 | 2013-04-14 09:43:42 EDT Bug fix to --bed and --exclude-bed to account for alt allele size. ---------------------------------------------------------------------------- r843 | auton1 | 2013-04-12 15:18:44 EDT Fix to --mask and --invert-mask when running with more than one chromosome (as reported by Iain Mathieson, April, 12th, 2013). ---------------------------------------------------------------------------- r842 | petulda | 2013-04-12 04:36:41 EDT Fix in vcf-contrast plus it now handles haploid genotypes. ---------------------------------------------------------------------------- r841 | petulda | 2013-04-11 09:29:05 EDT Split multiallelic indels before normalizing when matching against alleles from the annotation file ---------------------------------------------------------------------------- r840 | petulda | 2013-04-11 07:25:38 EDT vcf-annotate: Fix in annotating of multiallelic sites ---------------------------------------------------------------------------- r839 | petulda | 2013-04-02 11:29:39 EDT vcf-merge via Vcf.pm: do not get fooled by non-variant sites when determining ploidy ---------------------------------------------------------------------------- r838 | petulda | 2013-03-27 11:05:28 EDT Updated htslib documentation ---------------------------------------------------------------------------- r837 | auton1 | 2013-03-18 13:04:00 EDT Bug fix for calculating windowed diversity. ---------------------------------------------------------------------------- r836 | auton1 | 2013-03-18 12:10:13 EDT ---------------------------------------------------------------------------- r835 | auton1 | 2013-03-15 13:31:41 EDT ---------------------------------------------------------------------------- r834 | auton1 | 2013-03-15 13:13:53 EDT Bug fix for calculating windowed diversity when only using a subset of individuals in a file. ---------------------------------------------------------------------------- r833 | auton1 | 2013-02-26 16:19:09 EST Minor ---------------------------------------------------------------------------- r832 | auton1 | 2013-02-26 10:12:51 EST Fix for bug #42... --window-pi failed if very large windows used. ---------------------------------------------------------------------------- r831 | petulda | 2013-02-25 04:11:17 EST Fixed an example and added another one. ---------------------------------------------------------------------------- r830 | auton1 | 2013-02-22 16:50:08 EST Allow haploid individuals to be included in the calculation of --hap-r2. ---------------------------------------------------------------------------- r829 | auton1 | 2013-02-14 16:43:12 EST Refactoring of LD code to avoid excessive code duplication. ---------------------------------------------------------------------------- r828 | auton1 | 2013-02-14 11:46:22 EST Allow --chr and --not-chr to be used more than once to include/exclude multiple chromosomes. ---------------------------------------------------------------------------- r827 | auton1 | 2013-02-13 16:19:22 EST Small performance improvement to LD calculations. ---------------------------------------------------------------------------- r826 | auton1 | 2013-02-13 16:12:04 EST Small performance improvement to LD calculations. ---------------------------------------------------------------------------- r825 | auton1 | 2013-02-13 14:39:38 EST Minor follow-up to last commit. ---------------------------------------------------------------------------- r824 | auton1 | 2013-02-13 14:31:39 EST Added minimum distance option for LD calculation. ---------------------------------------------------------------------------- r823 | petulda | 2013-02-13 10:17:33 EST Updated online docs ---------------------------------------------------------------------------- r822 | auton1 | 2013-02-11 16:57:52 EST Minor clean up of code comments. ---------------------------------------------------------------------------- r821 | auton1 | 2013-02-11 16:21:38 EST Cleaned up Weir and Cockerham Fst code. Fixed a small bug that would stop first window being calculated. ---------------------------------------------------------------------------- r820 | auton1 | 2013-02-08 10:32:43 EST Fixed flipping of mean and weighted weir Fst estimates in log output. ---------------------------------------------------------------------------- r819 | auton1 | 2013-02-07 13:17:31 EST Output global value of Fst when running in windowed version. ---------------------------------------------------------------------------- r818 | petulda | 2013-02-05 02:50:50 EST Fixed month range in timestamp with append option (was 0..11). On behalf of Keiran Raine. ---------------------------------------------------------------------------- r817 | auton1 | 2013-01-26 14:25:43 EST Minor. ---------------------------------------------------------------------------- r816 | auton1 | 2013-01-26 14:24:18 EST Updated --bed and --exclude-bed to account for variant size when filtering. Variants that with any overlap of a window are included. (Bug #37) ---------------------------------------------------------------------------- r815 | auton1 | 2013-01-26 14:13:26 EST Added --fst-window-size and --fst-window-step options. Removed depreciated Fst options that used multiple VCF files. Updated documentation. Updated version number to 0.1.10.1. ---------------------------------------------------------------------------- r814 | petulda | 2013-01-22 05:41:49 EST Fix in Number=G tags handling, affects vcf-subset on haploid data ---------------------------------------------------------------------------- r813 | auton1 | 2013-01-21 12:18:07 EST Change License to LGPLv3. ---------------------------------------------------------------------------- r812 | petulda | 2012-12-24 03:44:46 EST vcf-subset: more types recognised with -t option; ref must be given explicitly. ---------------------------------------------------------------------------- r811 | petulda | 2012-12-20 04:45:09 EST Allow missing fields in replace_field ---------------------------------------------------------------------------- r810 | petulda | 2012-12-20 04:44:42 EST Use only phased GTs for haplotype assignment ---------------------------------------------------------------------------- r809 | petulda | 2012-12-11 09:50:54 EST Removed fill-rsIDs and vcf-filter from Makefile ---------------------------------------------------------------------------- r808 | petulda | 2012-12-10 08:29:30 EST INFO/TYPE with Number=A rather than Number=1 ---------------------------------------------------------------------------- r807 | auton1 | 2012-12-05 17:13:51 EST Don't count missing data when calculating expected homozygosity (bug fix to --het) ---------------------------------------------------------------------------- r806 | petulda | 2012-12-04 03:26:44 EST Vcf.pm: More informative error message with missing columns; vcf-phased-join: Allow different alleles at multiallelic sites ---------------------------------------------------------------------------- |
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From: Adam A. <ada...@gm...> - 2012-12-10 14:21:05
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This is a belated announcement of VCFtools v0.1.10, which was posted as a tarball last week. This version can be downloaded from here: http://sourceforge.net/projects/vcftools/ All users with earlier versions are encouraged to upgrade as soon as possible. Changes since the last release follow this email. Kind regards, Adam Auton - Increment version number to v0.1.10 [r805] by auton1 - Additional error reporting for stat call. [r804] by auton1 - vcf-fix-ploidy: reflect recent change in treatment of missing values in VCF::get_field [r803] by petulda - Make vcf-isec work in situations when the same file is given multiple times on the command line [r802] by petulda - Documented the new htslib VCF commands [r801] by petulda - Correctly convert "chr1" etc to "1" for PLINK conversion. [r800] by auton1 - Minor change to output more info when using --weir-fst-pop [r799] by auton1 - Bug fix for --geno-depth. Old values could be output when missing data included [r798] by auton1 - The validator drops the requirement of first matching bases in REF and ALT. [r797] by petulda - New option for vcf-sort, -t, to specify the temporary directory that the sorting will occur in [r796] by amarcket - Added a Makefile compiler flag to support files > 2Gb. [r795] by auton1 - Fix for multiallelic records and buffer boundary conditions. [r794] by petulda - New option: -H, --hard-filter [r793] by petulda - Handle missing PL and GT fields. Cleaned code a bit. [r792] by petulda - Fix: correct initialization at start of new chromosome; previously annotation records with small positions were ignored. [r791] by petulda - Added --BEAGLE-PL option. [r790] by auton1 - fill-fs: strip alleles' common prefix as well as suffix. [r789] by petulda - Fix: uniform length of flanking sequence in presence of superfluous padding bases [r788] by petulda - Allow missing sites in overlaps [r787] by petulda - Added a ! missing in the previous commit [r786] by petulda - New -n option to vcf-annotate; More thorough checking of alleles identify in annotation files;... [r785] by petulda - Updated repository link on main home page. [r783] by auton1 - Added the --hist-indel-len option. [r781] by amarcket - New --collapse option to vcf-merge and Dummy filter to vcf-annotate. [r779] by petulda - Use existing API for selective removal of filters and -r FILTER resets to PASS, not ".". [r778] by petulda - Added missing documentation for generic format fields. [r777] by petulda - vcf-fix-ploidy selects most likely alleles. [r776] by petulda - Allow out-of-range indexes in remove_field, the specification allows omitting empty fields. [r775] by petulda - Change to cpp makefile to only recompile changed files. [r774] by auton1 - Allow zero overlap between chunks and set the PS tag appropriately. [r773] by petulda - Include initial open errors in the validation summary. [r772] by petulda - If PL not available, use GT in vcf-contrast [r771] by petulda - close returns proper status now [r770] by petulda |
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From: Adam A. <ada...@gm...> - 2012-09-21 14:34:01
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Dear all, Due to an upgrade of the SourceForge software, the SVN repository used by VCFtools has moved. The new command to check out the latest version of the code is now: svn checkout https://svn.code.sf.net/p/vcftools/code vcftools If you are using the old address, please update to the new address as the old address will not reflect the latest developments. Many thanks, Adam -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Center 320, Bronx, New York 10461 Tel: +1 (718) 678 1038 |
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From: Adam A. <ada...@gm...> - 2012-05-10 13:36:07
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Dear all, We have just released VCFtools version 0.1.9, which is available for download at http://sourceforge.net/projects/vcftools/ . All users of previous versions are encouraged to upgrade as soon as possible. Kind regards, Adam -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Center 320, Bronx, New York 10461 Tel: +1 (718) 678 1038 |
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From: Adam A. <ada...@gm...> - 2012-01-23 15:36:45
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Dear all, Over the weekend, a new version of VCFtools was released and is available for download at https://sourceforge.net/projects/vcftools/. This version includes a number of changes and fixes that are listed below. Users are encouraged to upgrade to the new version as soon as possible. Many thanks, Adam Auton and Petr Danecek C++ module: - Ability to output VCF files to the stream via --recode-to-stream. - Fixed a bug in which a space was interpreted as a delimiter. - Added some missing documentation. Perl modules: - fill-fs: new script for annotating VCFs with flanking sequence - fill-ref-md5: new script for annotating VCFs with 'reference' and 'contig' tags recommended by VCFv4.1 - vcf-fix-newlines: new script for fixing newline representation - vcf-phased-join: new script for joining pre-phased VCFs - vcf-annotate: now also removes annotations and can apply user-defined filters - vcf-compare: changed output format, more stats reported and plots the results - vcf-query: significant speed up for some type of queries - vcf-sort: chromosomal ordering (1,2,10,MT,X rather than 1,10,2,MT,X) with new versions of unix sort - Vcf.pm: new set of API methods for faster access - some of the tools now work also with remote files -- Adam Auton Assistant Professor, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Price Center 320, Bronx, New York 10461 Tel: +1 (718) 678 1038 |
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From: Adam A. <ada...@gm...> - 2011-10-07 08:53:46
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Dear all, I have posted VCFtools version 0.1.7 on the sourceforge website ( https://sourceforge.net/projects/vcftools/). This version includes a number of bug fixes and enhancements to both C++ and Perl modules. Users are encouraged to upgrade as soon as possible. Kind regards, Adam -- Adam Auton Post-Doctoral Research Scientist, Wellcome Trust Centre for Human Genetics, University of Oxford Roosevelt Drive Oxford OX3 7BN UK |
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From: Adam A. <ada...@gm...> - 2011-07-11 08:58:57
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Dear all, I have posted VCFtools version 0.1.6 on the sourceforge website ( https://sourceforge.net/projects/vcftools/). This version includes a number of improvements to both the C++ and Perl modules. Importantly, the C++ module should now support VCFv4.1. Kind regards, Adam -- Adam Auton Post-Doctoral Research Scientist, Wellcome Trust Centre for Human Genetics, University of Oxford Roosevelt Drive Oxford OX3 7BN UK |
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From: Adam A. <ada...@gm...> - 2011-04-13 13:18:06
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Dear all, I have posted VCFtools version 0.1.5 on the sourceforge website ( https://sourceforge.net/projects/vcftools/). This version includes a number of improvements to both the C++ and Perl modules. C++ module: - Considerable performance improvements to PLINK file output (as well as other file formats). - Near-complete implementation of genotype-level filters. - General performance improvements and bug fixes. Perl module: - Support for the upcoming VCF4.1 specification. Kind regards, Adam -- Adam Auton Post-Doctoral Research Scientist, Wellcome Trust Centre for Human Genetics, University of Oxford Roosevelt Drive Oxford OX3 7BN UK |
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From: Adam A. <ada...@gm...> - 2011-02-02 09:56:34
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Dear all, I have posted VCFtools version 0.1.4 on the sourceforge website ( https://sourceforge.net/projects/vcftools/). This version includes a number of bug fixes, particularly to the C++ module, and it is recommended that all users upgrade. Also included are new options for reading zipped VCF files, which should be of use for users working with large files. Kind regards, Adam -- Adam Auton Post-Doctoral Research Scientist, Wellcome Trust Centre for Human Genetics, University of Oxford Roosevelt Drive Oxford OX3 7BN UK |
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From: Adam A. <ada...@gm...> - 2010-12-23 15:55:03
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Dear all, A new release of VCFtools (version 0.1.3.2) has just been posted on the sourceforge site. This release includes a number of bug fixes and feature enhancements to both the C++ binary and the Perl module. It is recommended that all users upgrade to this version, either by downloading from the sourceforge website ( https://sourceforge.net/projects/vcftools/), or via SVN. Kind regards, Adam Auton -- Adam Auton Post-Doctoral Research Scientist, Wellcome Trust Centre for Human Genetics, University of Oxford Roosevelt Drive Oxford OX3 7BN UK |
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From: Adrian J. <ori...@gm...> - 2010-12-13 23:48:44
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Dear Group, I am trying to annotate Dindel output in VCF format using SeattleSeq annotation server. Currently SeattleSeq annotatation server accepts only GATK Bed file with indels. GATK Bed file format is : chr1 556817 556817 +G:3/7 chr1 3535035 3535054 -TTCTGGGAGCTCCTCCCCC:9/21 chr1 3778838 3778838 +A:15/48 Where first line is an insertion at 556817 where 3 reads out of total 7 reads have an insertion +G chr13 108316677 . C AGTA 127 PASS DP=47;NF=0;NR=3;NRS=0;NFS=13;HP=1 GT:GQ 0/1:127 The above line is a row from Dindel VCF file. From this line, where can I get how many reads of total reads at this locus have GTA insertion. could any one please help here. thanks in advance. Adrian |
