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, 21:48, 15 June 2014
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| First you want to know what is in the bcf file. | | First you want to know what is in the bcf file. |
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− | vt peek all.genotypes.bcf | + | vt peek all.genotypes.bcf |
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| stats: no. of samples : 62 | | stats: no. of samples : 62 |
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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 |
| + | |
| + | 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] |
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| == Comparison with other data sets == | | == Comparison with other data sets == |