Mercurial > repos > jjohnson > bcftools_convert_to_vcf
comparison README.md @ 0:bca07db8f55c 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 20:47:33 -0400 |
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| -1:000000000000 | 0:bca07db8f55c |
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| 1 # bcftools (v1.3) | |
| 2 | |
| 3 Copied from branch bcftools1.2: | |
| 4 | |
| 5 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are | |
| 6 presented essentially as closely to the command line version as is useful. | |
| 7 | |
| 8 This may not appeal to all, if you'd like to see smaller and more dedicated | |
| 9 tools (e.g. "intersect", "union" and "complement" being separate tools instead | |
| 10 of all of them included in the "isec" tool,) please feel free to file an issue. | |
| 11 | |
| 12 Updated for bcftools v1.3 | |
| 13 | |
| 14 This was extended from the bcftools1.2 branch then greatly hand edited to | |
| 15 group params and manage param innteractions. | |
| 16 | |
| 17 In the macros.xml there are macros and tokens to handle file input and output. | |
| 18 These use the datatypes currently available in galaxy: Vcf and Bcf | |
| 19 The macros take care of bgzip and indexing of inputs. | |
| 20 | |
| 21 The convert command was split into 2 tools, "convert to vcf" and "convert from vcf" | |
| 22 | |
| 23 ## TODO: | |
| 24 | |
| 25 - stats needs a matplotlib tool dependency and pdflatex for generating a pdf of plots | |
| 26 - cnv needs a matplotlib tool dependency for generating images, then a means to consolidate those. | |
| 27 - cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf | |
| 28 - roh needs a more useful input.vcf for testing | |
| 29 - plugin color chrs | |
| 30 - plugin frameshifts | |
| 31 | |
| 32 ## Status | |
| 33 | |
| 34 The wrappers were automatically generated in bulk. That doesn't get them 100% | |
| 35 of the way there (e.g. meaningful test cases), so the rest of the process is a | |
| 36 bit slower. | |
| 37 | |
| 38 - [x] annotate | |
| 39 - [x] call | |
| 40 - [ ] cnv (needs real test data, needs plotting) | |
| 41 - [x] concat | |
| 42 - [x] consensus | |
| 43 - [x] convert from vcf | |
| 44 - [x] convert to vcf | |
| 45 - [x] filter | |
| 46 - [x] gtcheck | |
| 47 - [x] isec | |
| 48 - [x] merge | |
| 49 - [x] norm | |
| 50 - [x] query | |
| 51 - [x] query list samples | |
| 52 - [x] reheader | |
| 53 - [x] roh | |
| 54 - [x] stats (needs plotting) | |
| 55 - [x] view | |
| 56 - [ ] +color chrs | |
| 57 - [x] +counts | |
| 58 - [x] +dosage | |
| 59 - [x] +fill an ac | |
| 60 - [x] +fill tags | |
| 61 - [x] +fixploidy | |
| 62 - [ ] +frameshifts | |
| 63 - [x] +impute info | |
| 64 - [x] +mendelian | |
| 65 - [x] +missing2ref | |
| 66 - [x] +setgt | |
| 67 - [x] +tag2tag | |
| 68 - [x] +vcf2sex |