Mercurial > repos > jjohnson > bcftools_query
comparison README.md @ 0:bfea7fe50fd0 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 20:51:59 -0400 |
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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 |