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Update mane criteria based on Ensembl/ensembl-vep#1336
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@nuno-agostinho
nuno-agostinho authored Jan 10, 2023
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Showing 1 changed file with 12 additions and 12 deletions.
24 changes: 12 additions & 12 deletions root/documentation/vep.conf
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</flag_pick_allele_gene>
<pick_order>
type=String
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ].
default=mane,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].
default=mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
</pick_order>
<AncestralAllele>
type=Boolean
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</flag_pick_allele_gene>
<pick_order>
type=String
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ].
default=mane,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].
default=mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
</pick_order>
<AncestralAllele>
type=Boolean
Expand Down Expand Up @@ -763,8 +763,8 @@
</flag_pick_allele_gene>
<pick_order>
type=String
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ].
default=mane,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].
default=mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
</pick_order>
<AncestralAllele>
type=Boolean
Expand Down Expand Up @@ -1053,8 +1053,8 @@
</flag_pick_allele_gene>
<pick_order>
type=String
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ].
default=mane,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].
default=mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
</pick_order>
<AncestralAllele>
type=Boolean
Expand Down Expand Up @@ -1344,8 +1344,8 @@
</flag_pick_allele_gene>
<pick_order>
type=String
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ].
default=mane,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].
default=mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
</pick_order>
<AncestralAllele>
type=Boolean
Expand Down Expand Up @@ -1653,8 +1653,8 @@
</flag_pick_allele_gene>
<pick_order>
type=String
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane ].
default=mane,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
description=Comma-separated list with order of criteria (and the list of criteria) applied when choosing a block of annotation data with one of the following options: <b>pick</b>, <b>pick_allele</b>, <b>per_gene</b>, <b>pick_allele_gene</b>, <b>flag_pick</b>, <b>flag_pick_allele</b>, <b>flag_pick_allele_gene</b>. See <a target="_blank" href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html\#pick_options">this page</a> for the default order. Valid criteria are: [ canonical appris tsl biotype ccds rank length mane_select mane_clinical ].
default=mane_select,<wbr>mane_clinical,<wbr>canonical,<wbr>appris,<wbr>tsl,<wbr>biotype,<wbr>ccds,<wbr>rank,<wbr>length
</pick_order>
<AncestralAllele>
type=Boolean
Expand Down

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