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VCFgenotype-to-haplotype:

Convert genotype-based phased alleles into haplotype alleles (Galaxy Version 1.0.0_rc3+galaxy0)

Tool Parameters

Choose the source for the reference genome

Select reference genome *

Please provide a value for this option.

Select VCF dataset * required

No datasets with vcf elements available

compare records up to this many bp away - optional

--window-size option (default = 30)

What to report?

--only-variants option

Additional Options

Email notification

Send an email notification when the job completes.

Help

Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.

The options are:

-w, --window-size N     Merge variants at most this many bp apart (default 30)
-o, --only-variants     Don't output the entire haplotype, just concatenate
                        REF/ALT strings (delimited by ":")

Vcfgeno2haplo is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).

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