Changes between Version 5 and Version 6 of SOPs/vcf_manipulation

Timestamp:

06/05/14 09:47:41 (11 years ago)

Author:

gbell

Comment:

--

SOPs/vcf_manipulation

@@ -32 +32 @@
 }}}
 
-Annotate a VCF file (applying all filters with default values):
+Annotate a VCF file using [http://vcftools.sourceforge.net/perl_module.html#vcf-annotate vcf-annotate]
 {{{
-cat Variants_all_samples.raw.vcf | vcf-annotate -f + > Variants_all_samples.withTags.vcf
+# Apply all filters with default values:
+vcf-annotate -f + Variants_all_samples.raw.vcf > Variants_all_samples.withTags.vcf
+# Apply all filters with default values except for specified ones (MinAB(a) = 10; MinDP(b) = 20):
+vcf-annotate -f +/a=10/d=20 Variants_all_samples.raw.vcf > Variants_all_samples.withTags.vcf
+# Add custom filter(s) as described in file "My_filters.txt":
+vcf-annotate -f My_filters.txt Variants_all_samples.raw.vcf > Variants_all_samples.withTags.vcf
 }}}
+
+For the last command, My_filters.txt contains a filter (such as an example one that calculates PLdiff values for 1/1 - 0/0 and 1/1 - 0/1, making sure that each difference is greater than 20).  In this case, the filter is designed for selection, rather than filtering out. [[BR]]
+For more examples, go to [http://vcftools.sourceforge.net/perl_module.html#vcf-annotate vcf-annotate] and click on "Read even more".
+{{{
+{
+    tag      => 'FORMAT/PL',
+    name     => 'GoodPLdiff',
+    desc     => 'Homozygote alternate and PLdiff greater than 20',
+    apply_to => 'all',
+    test     => sub {
+            for my $pl (@$MATCH)
+            {
+                my @pls = split(/,/,$pl);
+                if ( ($pls[2]-$pls[0])>20 && ($pls[1]-$pls[0])>20 ) { return $FAIL; }
+            }
+        return $PASS;
+    },
+},
+}}}
+
 
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