1,102
edits
Changes
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Revision as of 16:34, 16 June 2014
, 16:34, 16 June 2014→Summary
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.
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.
vt peek all.genotypes.bcf -f "FILTER.TPASS"
vt peek all.genotypes.bcf -f "FILTER.PASS"
stats: no. of samples : 62
stats: no. of samples : 62
#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"
#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"
#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"
#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)"
== Comparison with other data sets ==
== Comparison with other data sets ==
