Mercurial > repos > iuc > bcftools_call

comparison README.md @ 1:8959eda17fca draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:01:07 -0400
parents a531317a3527
children 0a564427739d
comparison
equal deleted inserted replaced
0:a531317a3527 1:8959eda17fca
1 # bcftools (v1.2) 1 # bcftools (v1.3)
2
3 Copied from branch bcftools1.2:
2 4
3 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are 5 This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
4 presented essentially as closely to the command line version as is useful. 6 presented essentially as closely to the command line version as is useful.
5 7
6 This may not appeal to all, if you'd like to see smaller and more dedicated 8 This may not appeal to all, if you'd like to see smaller and more dedicated
7 tools (e.g. "intersect", "union" and "complement" being separate tools instead 9 tools (e.g. "intersect", "union" and "complement" being separate tools instead
8 of all of them included in the "isec" tool,) please feel free to file an issue. 10 of all of them included in the "isec" tool,) please feel free to file an issue.
9 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
10 ## TODO: 23 ## TODO:
11 24
12 - Galaxy needs datatypes for bcf and vcf files, block-gzipped and uncompressed. 25 - stats needs a matplotlib tool dependency and pdflatex for generating a pdf of plots
13 - Galaxy needs to automatically index those files with tabix 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
14 31
15 ## "Complete" Wrappers 32 ## Status
16 33
17 The wrappers were automatically generated in bulk. That doesn't get them 100% 34 The wrappers were automatically generated in bulk. That doesn't get them 100%
18 of the way there (e.g. meaningful test cases), so the rest of the process is a 35 of the way there (e.g. meaningful test cases), so the rest of the process is a
19 bit slower. 36 bit slower.
20 37
21 - bcftools call 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