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Revision as of 03:15, 17 June 2014
, 03:15, 17 June 2014→Summary
>=3 alleles (ins/del) : 0 (-nan) [0/0] <br>
>=3 alleles (ins/del) : 0 (-nan) [0/0] <br>
no. of observed variants : 720
no. of observed variants : 720
* Our VCF only contains INDELs so there are lots of <code>0 (-nan) [0/0]</code> values in the output. <code>vt</code> can be used to analyze VCFs with more variants than just INDELs.
* Our VCF only contains only biallelic INDELs so there are lots of <code>0 (-nan) [0/0]</code> values in the output. <code>vt</code> can be used to analyze VCFs with more variants than just INDELs.
The variants have filter labels. PASS meaning a temporary pass and overlap, meaning that the variants are overlapping with another variant, implying multiallelicity.
The variants have filter labels. PASS meaning a passed variant and overlap, meaning that the variants are overlapping with another variant, implying multiallelicity.
We can count the number of variants with different filters with the following commands.
We can count the number of variants with different filters with the following commands.
