Mercurial > repos > jjohnson > bcftools_roh
annotate README.md @ 0:ee03050edc3d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author | jjohnson |
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date | Sat, 25 Jun 2016 20:52:49 -0400 |
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ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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1 # bcftools (v1.3) |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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2 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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3 Copied from branch bcftools1.2: |
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4 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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5 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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6 presented essentially as closely to the command line version as is useful. |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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7 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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8 This may not appeal to all, if you'd like to see smaller and more dedicated |
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9 tools (e.g. "intersect", "union" and "complement" being separate tools instead |
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10 of all of them included in the "isec" tool,) please feel free to file an issue. |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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11 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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12 Updated for bcftools v1.3 |
ee03050edc3d
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13 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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14 This was extended from the bcftools1.2 branch then greatly hand edited to |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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15 group params and manage param innteractions. |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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16 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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17 In the macros.xml there are macros and tokens to handle file input and output. |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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18 These use the datatypes currently available in galaxy: Vcf and Bcf |
ee03050edc3d
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19 The macros take care of bgzip and indexing of inputs. |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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20 |
ee03050edc3d
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21 The convert command was split into 2 tools, "convert to vcf" and "convert from vcf" |
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22 |
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23 ## TODO: |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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24 |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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25 - stats needs a matplotlib tool dependency and pdflatex for generating a pdf of plots |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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26 - cnv needs a matplotlib tool dependency for generating images, then a means to consolidate those. |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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27 - cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf |
ee03050edc3d
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28 - roh needs a more useful input.vcf for testing |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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29 - plugin color chrs |
ee03050edc3d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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30 - plugin frameshifts |
ee03050edc3d
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31 |
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32 ## Status |
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33 |
ee03050edc3d
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34 The wrappers were automatically generated in bulk. That doesn't get them 100% |
ee03050edc3d
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35 of the way there (e.g. meaningful test cases), so the rest of the process is a |
ee03050edc3d
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36 bit slower. |
ee03050edc3d
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37 |
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38 - [x] annotate |
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39 - [x] call |
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40 - [ ] cnv (needs real test data, needs plotting) |
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41 - [x] concat |
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42 - [x] consensus |
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43 - [x] convert from vcf |
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44 - [x] convert to vcf |
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45 - [x] filter |
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46 - [x] gtcheck |
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47 - [x] isec |
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48 - [x] merge |
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49 - [x] norm |
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50 - [x] query |
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51 - [x] query list samples |
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52 - [x] reheader |
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53 - [x] roh |
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54 - [x] stats (needs plotting) |
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55 - [x] view |
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56 - [ ] +color chrs |
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57 - [x] +counts |
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58 - [x] +dosage |
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59 - [x] +fill an ac |
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60 - [x] +fill tags |
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61 - [x] +fixploidy |
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62 - [ ] +frameshifts |
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63 - [x] +impute info |
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64 - [x] +mendelian |
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65 - [x] +missing2ref |
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66 - [x] +setgt |
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67 - [x] +tag2tag |
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68 - [x] +vcf2sex |