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Revision as of 15:42, 9 July 2014
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The following section details some simple analyses we can perform.
The following section details some simple analyses we can perform.
===Summary===
First you want to know what is in the vcf file.
First you want to know what is in the vcf file.
${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)"
${GC}/bin/vt peek ${OUT}/final/all.genotypes.vcf.gz -f "FILTER.PASS&&(LEN==4||DLEN==3)"
== Comparison with other data sets ==
=== Comparison with other data sets ===
It is usually useful to examine the call sets against known data sets for the passed variants.
It is usually useful to examine the call sets against known data sets for the passed variants.
This analysis supports filters too.
This analysis supports filters too.
==Normalization==
===Normalization===
A slight digression here, when analyzing indels, it is important to normalize it. While it is a simple concept,
A slight digression here, when analyzing indels, it is important to normalize it. While it is a simple concept,
