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Revision as of 21:48, 15 June 2014
, 21:48, 15 June 2014→Summary
First you want to know what is in the bcf file.
First you want to know what is in the bcf file.
vt peek all.genotypes.bcf
vt peek all.genotypes.bcf
stats: no. of samples : 62
stats: no. of samples : 62
>=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
The variants have filter labels TPASS meaning a temporary pass and overlap, meaning that the variants are overlapping with another variant, implying multiallelicity.
We can count the number of variants with the following commands.
vt peek all.genotypes.bcf -f "FILTER.TPASS"
stats: no. of samples : 62
no. of chromosomes : 1 <br>
no. Indels : 584
2 alleles (ins/del) : 584 (0.69) [239/345]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
vt peek all.genotypes.bcf -f "FILTER.overlap"
stats: no. of samples : 62
no. of chromosomes : 1 <br>
no. Indels : 136
2 alleles (ins/del) : 136 (1.89) [89/47] #notice the difference insertion deletion ratios differences
>=3 alleles (ins/del) : 0 (-nan) [0/0]
== Comparison with other data sets ==
== Comparison with other data sets ==
