... | ... | @@ -107,7 +107,7 @@ Example : |
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### --assembly-annot [mandatory]
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The annotation option attributes are :
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* file* : contigs annotation file in GFF3 [http://gmod.org/wiki/GFF3] with some specials attributes.
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* file* : contigs annotation file in [GFF3](http://gmod.org/wiki/GFF3) with some specials attributes.
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* software-name* : [string] name of the software with which the annotation has been produced
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* software-parameters* : [string] annotation software parameters
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* software-version* : [string] annotation software version
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... | ... | @@ -178,7 +178,7 @@ This file contains for each the variation informations of the contigs contigs : |
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If the VCF file has been produced using [GATK](http://www.broadinstitute.org/gatk/), the allelic count per library will be extracted from the VCF file.
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Here is the list of attributes for this options :
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* file : in VCF [http://vcftools.sourceforge.net/specs.html]
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* file : in [VCF](http://vcftools.sourceforge.net/specs.html)
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* software-name : [string] detection software name
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* software-parameters : [string] detection software parameters
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* software-version : [string] detection software version
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... | ... | @@ -200,7 +200,7 @@ This option was design to store SNP annotations. Its usually produced by alignme |
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* related gene
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Here is the list of attributes of this options :
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* file : in GFF3 [http://gmod.org/wiki/GFF3]
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* file : in [GFF3](http://gmod.org/wiki/GFF3)
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* software-name : [string] detection software name
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* software-parameters : [string] detection software parameters
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* software-version : [string] detection software version
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... | ... | |