How are two alleles typically represented in a whole genome sequence?

How are two alleles typically represented in a whole genome sequence?

0

I apologize in advance if this is a silly question – but I am trying to understand how two inherited variants of a gene are represented in typical whole genome sequencing formats (VCF, FASTA/Q).

Here is one example illustrating my confusion, using an SNP VCF from a WGS. Take TAS2R38.. GRCh37.p13 puts the gene’s reference location at chr7:g.141672431 – chr7:g.141673573.

Using bcftools, if I call:

bcftools view genome.filtered.snp.vcf.gz 7:141673345-141673345
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
7   141673345   .   C   G   1434.3  PASS

How could I view the SNP, if any, from the other copy of the gene? And which allele am I viewing when I do the above?


genetics


inheritance


sequencing

• 22 views

Read more here: Source link