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6 bytes removed
, 16:34, 16 June 2014
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| no. of observed variants : 720 | | no. of observed variants : 720 |
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− | The variants have filter labels TPASS 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 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. | | We can count the number of variants with the following commands. |
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− | vt peek all.genotypes.bcf -f "FILTER.TPASS" | + | vt peek all.genotypes.bcf -f "FILTER.PASS" |
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| stats: no. of samples : 62 | | stats: no. of samples : 62 |
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| #passed singletons only | | #passed singletons only |
− | vt peek all.genotypes.bcf -f "FILTER.TPASS&&INFO.AC==1" | + | vt peek all.genotypes.bcf -f "FILTER.PASS&&INFO.AC==1" |
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| #passed indels of length 1 only | | #passed indels of length 1 only |
− | vt peek all.genotypes.bcf -f "FILTER.TPASS&&LEN==1" | + | vt peek all.genotypes.bcf -f "FILTER.PASS&&LEN==1" |
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| #passed indels of length >4 | | #passed indels of length >4 |
− | vt peek all.genotypes.bcf -f "FILTER.TPASS&&LEN>1" | + | vt peek all.genotypes.bcf -f "FILTER.PASS&&LEN>1" |
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| #passed singletons of length 4 or insertions of length 3 | | #passed singletons of length 4 or insertions of length 3 |
− | vt peek all.genotypes.bcf -f "FILTER.TPASS&&(LEN==4||DLEN==3)" | + | vt peek all.genotypes.bcf -f "FILTER.PASS&&(LEN==4||DLEN==3)" |
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| == Comparison with other data sets == | | == Comparison with other data sets == |