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This command creates a database called "my_database.db" and inserts the SNP position table into it. If "my_database.db" had existed already, it would drop the snp_pos table in it, and insert yours in its place.
This command creates a database called "my_database.db" and inserts the SNP position table into it. If "my_database.db" had existed already, it would drop the snp_pos table in it, and insert yours in its place.
One special note about adding SNP position tables: a refsnp_trans table will automatically be created for you, where each SNP maps to itself. If you have a list of SNPs from previous builds that you would like to map to a SNP in the current build, you can then insert your own refsnp_trans table (see *LINK*).
One special note about adding SNP position tables: a refsnp_trans table will automatically be created for you, where each SNP maps to itself. If you have a list of SNPs from previous builds that you would like to map to a SNP in the current build, you can then insert your own refsnp_trans table (see below for more information on this table.)
==== Inserting refsnp_trans ====
The refsnp_trans table looks like the following:
{| width="75%" cellspacing="0" cellpadding="5" border="1" class="sortable"
|-
! scope="col" | rs_orig
! scope="col" | rs_current
|-
| rs840 || rs715
|-
| rs1086 || rs940
|-
| rs1234 || rs1067
|}
The first column contains SNP names from older genome builds, and the rs_current column contains SNP names from the current genome build (i.e., the build your database file is anchored to.)
Inserting this table into your database is simply then:
<pre> dbmeister.py --db my_database.db --trans my_snp_translations_file </pre>
You will want to execute this command AFTER inserting the snp_pos table, since that command drops the existing translation table.
==== Inserting refFlat ====
==== Inserting refFlat ====
The refFlat table mirrors what is currently supplied by the refFlat table in the UCSC database. The file should look like:
==== Inserting recomb_rate ====
==== Inserting recomb_rate ====
==== Inserting snp_set ====
==== Inserting snp_set ====
=== Changing m2zfast.conf settings ===
=== Changing m2zfast.conf settings ===
