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You may also work with vcf.gz, just name the output as *.vcf.gz. But it will be slower with vt.
You may also work with vcf.gz, just name the output as *.vcf.gz. But it will be slower with vt.
==Peek==
You can see what you have in the file with:
vt peek mills.genotypes.bcf
You can also focus on a chromosome:
vt peek mills.genotypes.bcf -i 20
Or with just passed variants:
vt peek mills.genotypes.bcf -i 20 -f PASS
Or with failed variants:
vt peek mills.genotypes.bcf -i 20 -f ~PASS
Or with just 1bp indels:
vt peek mills.genotypes.bcf -i 20 -f "PASS&&DLEN==1"
Or with just 1bp deletions:
vt peek mills.genotypes.bcf -i 20 -f "PASS&&LEN==-1"
Or with just biallelic 1bp indels:
vt peek mills.genotypes.bcf -i 20 -f "PASS&&N_ALLELE==2&&LEN==1"
Or with just biallelic 1bp indels that are somewhat rare:
vt peek mills.sites.bcf -f "PASS&&N_ALLELE==2&&LEN==1&&INFO.AF<0.03"
Or with just biallelic 1bp indels that are somewhat rare with sanity checking:
vt peek mills.sites.bcf -f "PASS&&N_ALLELE==2&&LEN==1&&INFO.AC/INFO.AN<0.03"
==Normalization==
==Normalization==
number of duplicate variants found for some of the 1000 Genomes Trio High Coverage call sets.
number of duplicate variants found for some of the 1000 Genomes Trio High Coverage call sets.
Although left alignment seems to be a trivial concept, it is easily overlooked and remain a common
Although left alignment seems to be a trivial concept, it is easily overlooked and remain a common
mistake. Another example is the Mills et al. data set which followed up with 10004 Indels for validation.
mistake.
{| class="wikitable"
{| class="wikitable"
| 7541
| 7541
|}
|}
Another example is the Mills et al. data set which followed up with 10004 Indels for validation.
Out of 9996 passed variants, it was found that after normalization, only 8904 distinct Indels remain
- about a loss of 11% of variant thought distinct.
==Coding regions==
==Coding regions==
