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Revision as of 16:47, 16 June 2014
, 16:47, 16 June 2014→Normalization
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
no. of chromosomes : 1 <br>
no. of chromosomes : 1 <br>
no. Indels : 136
no. Indels : 136
2 alleles (ins/del) : 136 (1.89) [89/47] #notice the difference insertion deletion ratios differences
2 alleles (ins/del) : 136 (1.89) [89/47] #notice the difference in insertion deletion ratios
>=3 alleles (ins/del) : 0 (-nan) [0/0]
>=3 alleles (ins/del) : 0 (-nan) [0/0]
#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 ==
It is usually useful to examine the call sets against known data sets for the passed variants.
It is usually useful to examine the call sets against known data sets for the passed variants.
vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "PASS"
vt profile_indels -g indel.reference.txt -r hs37d5.fa all.genotypes.bcf -i 22:36000000-37000000 -f "PASS"
data set
data set
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity.
vt profile_indels -g /net/fantasia/home/atks/ref/vt/grch37/indel.reference.txt -r /net/fantasia/home/atks/ref/vt/grch37/hs37d5.fa run/final/all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS"
vt profile_indels -g indel.reference.txt -r hs37d5.fa all.genotypes.bcf -i 22:36000000-37000000 -f "~PASS"
data set
data set
To normalize and remove duplicate variants:
To normalize and remove duplicate variants:
vt normalize mills.genotypes.bcf -r ~/ref/vt/grch37/hs37d5.fa | vt mergedups - -o mills.normalized.genotypes.bcf
vt normalize mills.genotypes.bcf -r hs37d5.fa | vt mergedups - -o mills.normalized.genotypes.bcf
and you will observe that 3994 variants had to be left aligned and 1092 variants were removed.
and you will observe that 3994 variants had to be left aligned and 1092 variants were removed.
