ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
User contributions for Thorfinn
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25 September 2012
- 17:4117:41, 25 September 2012 diff hist +450 Filters →Selected Sites
- 16:3216:32, 25 September 2012 diff hist +1 Installation →Download
- 16:3216:32, 25 September 2012 diff hist 0 ANGSD No edit summary
- 03:0003:00, 25 September 2012 diff hist +76 Genotype Likelihoods →output genotype likelihoods
- 02:3802:38, 25 September 2012 diff hist +211 Change log →Version notes
- 02:3702:37, 25 September 2012 diff hist +56 Genotype Likelihoods →soapSNP
- 02:3502:35, 25 September 2012 diff hist +81 Genotype Likelihoods →options
- 02:3502:35, 25 September 2012 diff hist −166 Genotype Likelihoods →options
- 02:3402:34, 25 September 2012 diff hist +1 ANGSD No edit summary
22 September 2012
- 23:3523:35, 22 September 2012 diff hist −60 SFS Estimation →realSFS
- 19:4319:43, 22 September 2012 diff hist +1 Installation →Unix
- 19:4219:42, 22 September 2012 diff hist +2 Installation →Download
- 19:4219:42, 22 September 2012 diff hist +86 Installation →Download
- 19:3919:39, 22 September 2012 diff hist +45 ANGSD No edit summary
2 July 2012
- 10:3710:37, 2 July 2012 diff hist +559 Genotype Likelihoods →soapSNP
29 June 2012
- 14:3714:37, 29 June 2012 diff hist −16 Regionfile No edit summary current
- 14:3614:36, 29 June 2012 diff hist −1 Regionfile No edit summary
- 14:3614:36, 29 June 2012 diff hist +664 N Regionfile Created page with "When your inputfile is bam files, then you can specify region You can specify a specific region using the following 3 ways: <examople> ./angsd -bam bamfiles.list -r chr20: ...."
22 June 2012
- 21:1821:18, 22 June 2012 diff hist +137 N Glf files Created page with "DRAGON ;-doGlf 1; tglf binary 10xdouble per sample ;-doGlf 2; beagle output gz requires -doMajorMinor 1/2 ;-doGlf otehrwise text output"
- 15:0315:03, 22 June 2012 diff hist +3 Genotype Likelihoods →Kim et al.
- 15:0215:02, 22 June 2012 diff hist +22 Genotype Likelihoods →soapSNP
19 June 2012
- 13:0413:04, 19 June 2012 diff hist +587 Filters No edit summary
- 13:0113:01, 19 June 2012 diff hist +900 Filters No edit summary
- 12:5812:58, 19 June 2012 diff hist +428 Filters No edit summary
- 11:4811:48, 19 June 2012 diff hist +114 Filters No edit summary
- 11:4211:42, 19 June 2012 diff hist 0 Filters No edit summary
- 11:4211:42, 19 June 2012 diff hist −9 Filters No edit summary
- 11:4211:42, 19 June 2012 diff hist +2 Filters No edit summary
- 11:4111:41, 19 June 2012 diff hist +342 N Filters Created page with "In most analysis you are only interested in a subset of sites and not all sites. Currently we have the following filter options. 1. ;-minMaf float: only work with sites with..."
- 11:3411:34, 19 June 2012 diff hist +107 SNP Calling No edit summary current
- 11:3311:33, 19 June 2012 diff hist +444 SNP Calling No edit summary
- 11:2011:20, 19 June 2012 diff hist +94 Allele Frequencies →Estimator from sequencing data
- 11:1811:18, 19 June 2012 diff hist +73 Genotype calling No edit summary
- 11:1511:15, 19 June 2012 diff hist +107 N SNP Calling Created page with "angsd can estimate and LRT for the site being variable. This works in tandem with -doMAF and -doMajorMinor."
- 11:0111:01, 19 June 2012 diff hist −265 SFS Estimation →Full example for simulating nextgen data and estimating SFS (somewhat deprecated should use sfstools now)
- 10:3410:34, 19 June 2012 diff hist +31 SFS Estimation →realSFS
- 10:3310:33, 19 June 2012 diff hist −41 SFS Estimation →realSFS
- 10:3110:31, 19 June 2012 diff hist −2 Input →tglf
- 10:3010:30, 19 June 2012 diff hist −6 Input →tglf
- 10:3010:30, 19 June 2012 diff hist +258 Input →tglf
- 10:2710:27, 19 June 2012 diff hist +10 Input →genotype likelihood files
- 10:2610:26, 19 June 2012 diff hist +461 Input →genotype likelihood files
- 10:2010:20, 19 June 2012 diff hist 0 Input →optional arguments
- 10:1910:19, 19 June 2012 diff hist −38 Input →bam files
- 10:1710:17, 19 June 2012 diff hist +1 Input No edit summary
14 June 2012
- 12:3712:37, 14 June 2012 diff hist +7 N Major Minor Created page with "SuX CuX"
1 June 2012
- 08:1508:15, 1 June 2012 diff hist +126 ANGSD →Commands
- 08:1308:13, 1 June 2012 diff hist +22 ANGSD →Commands
- 08:1208:12, 1 June 2012 diff hist +293 ANGSD →Commands
- 08:0808:08, 1 June 2012 diff hist +20 ANGSD No edit summary