Question: Understanding SNP variant output
0
gravatar for Ada
12 days ago by
Ada10
Ada10 wrote:
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT

What does the REF and ALT refer to in extraction of variants?

ADD COMMENTlink modified 12 days ago by reza.jabal420 • written 12 days ago by Ada10
2

see https://samtools.github.io/hts-specs/VCFv4.2.pdf

ADD REPLYlink written 12 days ago by Pierre Lindenbaum129k
2
gravatar for reza.jabal
12 days ago by
reza.jabal420
New York, USA
reza.jabal420 wrote:

In re-sequencing applications such as Whole-exome/Genome sequencing (WES/WGS), we align the sequenced contigs against a reference genome which is perceived as ground truth for the correct letter at each position. The REF represents the reference allele, and ALT represent anything else that is not a reference allele (also called alternative!). These two terms are occasionally confused with Major and Minor allele that rather have population connotation.

To familiarize yourself with the file format you are showing I recommend reading the Variant Call Format (VCF) specifications.

ADD COMMENTlink written 12 days ago by reza.jabal420
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