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+# bcftools (v1.3)
+
+Copied from branch bcftools1.2:
+
+This aims to be a "faithful" rendering of the bcftool suite. I.e. options are
+presented essentially as closely to the command line version as is useful.
+
+This may not appeal to all, if you'd like to see smaller and more dedicated
+tools (e.g. "intersect", "union" and "complement" being separate tools instead
+of all of them included in the "isec" tool,) please feel free to file an issue.
+
+Updated for bcftools v1.3
+
+This was extended from the bcftools1.2 branch then greatly hand edited to
+group params and manage param innteractions.
+
+In the macros.xml there are macros and tokens to handle file input and output.
+These use the datatypes currently available in galaxy: Vcf and Bcf
+The macros take care of bgzip and indexing of inputs.
+
+The convert command was split into 2 tools, "convert to vcf" and "convert from vcf"
+
+## TODO:
+
+- stats needs a matplotlib tool dependency  and pdflatex for generating a pdf of plots
+- cnv needs a matplotlib tool dependency for generating images, then a means to consolidate those.
+- cnv needs an input.vcf for testing, runs with bcftools cnv -s "HG00101" -o 'HG00101/' -p 5 mpileup.vcf
+- roh needs a more useful input.vcf for testing
+- plugin color chrs
+- plugin frameshifts
+
+## Status
+
+The wrappers were automatically generated in bulk. That doesn't get them 100%
+of the way there (e.g. meaningful test cases), so the rest of the process is a
+bit slower.
+
+- [x] annotate
+- [x] call
+- [ ] cnv (needs real test data, needs plotting)
+- [x] concat
+- [x] consensus
+- [x] convert from vcf
+- [x] convert to vcf
+- [x] filter
+- [x] gtcheck
+- [x] isec
+- [x] merge
+- [x] norm
+- [x] query
+- [x] query list samples
+- [x] reheader
+- [x] roh
+- [x] stats (needs plotting)
+- [x] view
+- [ ] +color chrs
+- [x] +counts
+- [x] +dosage
+- [x] +fill an ac
+- [x] +fill tags
+- [x] +fixploidy
+- [ ] +frameshifts
+- [x] +impute info
+- [x] +mendelian
+- [x] +missing2ref
+- [x] +setgt
+- [x] +tag2tag
+- [x] +vcf2sex