tutorial

README.md

@@ -18,6 +18,12 @@ the files you need:
 SESSIONDIR=/home/formacion/COMUNES/IAMZ/data/CIHEAM/sessions/variant_annotation
 ~~~~
 
+And make sure python3 can be found:
+
+~~~~ {.bash}
+alias python3='/home/formacion/COMUNES/IAMZ/soft/python-3.4.2/bin/python3.4'
+~~~~
+
 ### Slicing and dicing of VCF files
 
 VCF files can get very big. Being able to manipulate them and extract
@@ -28,7 +34,7 @@ called variants of chromosome 18, bgzip-ping them on-the-fly, and then
 indexing that file with tabix:
 
 ~~~~ {.bash}
-tabix -h /home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/allbt.vcf.gz 18 | bgzip >BT18.vcf.gz
+tabix -h $SESSIONDIR/allbt.vcf.gz 18 | bgzip >BT18.vcf.gz
 tabix -p vcf BT18.vcf.gz
 ~~~~
 

Tutorial.html

@@ -34,9 +34,11 @@ code > span.er { color: #ff0000; font-weight: bold; }
 <span class="kw">cd</span> annotation_session</code></pre>
 <p>Create an Env.Var. to the communal session directory that holds some of the files you need:</p>
 <pre class="sourceCode bash"><code class="sourceCode bash"><span class="ot">SESSIONDIR=</span>/home/formacion/COMUNES/IAMZ/data/CIHEAM/sessions/variant_annotation</code></pre>
+<p>And make sure python3 can be found:</p>
+<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">alias</span> python3=<span class="st">&#39;/home/formacion/COMUNES/IAMZ/soft/python-3.4.2/bin/python3.4&#39;</span></code></pre>
 <h3 id="slicing-and-dicing-of-vcf-files">Slicing and dicing of VCF files</h3>
 <p>VCF files can get very big. Being able to manipulate them and extract relevant information is important. In practice, flat text files such as VCF are currently the basis for further analysis - see the Imputation and Population practical sessions. The first task involves selecting all called variants of chromosome 18, bgzip-ping them on-the-fly, and then indexing that file with tabix:</p>
-<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">tabix</span> -h /home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/allbt.vcf.gz 18 <span class="kw">|</span> <span class="kw">bgzip</span> <span class="kw">&gt;</span>BT18.vcf.gz
+<pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">tabix</span> -h <span class="ot">$SESSIONDIR</span>/allbt.vcf.gz 18 <span class="kw">|</span> <span class="kw">bgzip</span> <span class="kw">&gt;</span>BT18.vcf.gz
 <span class="kw">tabix</span> -p vcf BT18.vcf.gz</code></pre>
 <p>Have a look at what is inside this file:</p>
 <pre class="sourceCode bash"><code class="sourceCode bash"><span class="kw">gunzip</span> -c BT18.vcf.gz <span class="kw">|</span> <span class="kw">grep</span> -v <span class="st">&#39;^##&#39;</span> <span class="kw">|</span> <span class="kw">more</span></code></pre>

Tutorial.wiki

@@ -13,13 +13,17 @@ Create an Env.Var. to the communal session directory that holds some of the file
 <source lang='bash'>
 SESSIONDIR=/home/formacion/COMUNES/IAMZ/data/CIHEAM/sessions/variant_annotation
 </source>
+And make sure python3 can be found:
+<source lang='bash'>
+alias python3='/home/formacion/COMUNES/IAMZ/soft/python-3.4.2/bin/python3.4'
+</source>
 
 === Slicing and dicing of VCF files ===
 
 VCF files can get very big. Being able to manipulate them and extract relevant information is important. In practice, flat text files such as VCF are currently the basis for further analysis - see the Imputation and Population practical sessions. The first task involves selecting all called variants of chromosome 18, bgzip-ping them on-the-fly, and then indexing that file with tabix:
 
 <source lang='bash'>
-tabix -h /home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/allbt.vcf.gz 18 | bgzip >BT18.vcf.gz
+tabix -h $SESSIONDIR/allbt.vcf.gz 18 | bgzip >BT18.vcf.gz
 tabix -p vcf BT18.vcf.gz
 </source>