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15 bytes added
, 03:15, 17 June 2014
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| >=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. |
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− | 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. |
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| 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. |