Question

Fields In The Vcf File

0

Entering edit mode

10.1 years ago

hudailkom47 • 0

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    /home/output.bam
10    389659    .    T    C    4.13    .    DP=2;RPB=9.668049e-01;AF1=0.4999;AC1=1;DP4=0,1,0,1;MQ=42;FQ=4.93;PV4=1,1,1,1    GT:PL:GQ    0/1:32,0,35:31

what mean field "POS" it? what does this mean position? what the position is?

snp vcf • 3.5k views

ADD COMMENT • link updated 10.1 years ago by Devon Ryan 104k • written 10.1 years ago by hudailkom47 • 0

0

Entering edit mode

http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 https://github.com/samtools/hts-specs http://en.wikipedia.org/wiki/Variant_Call_Format http://faculty.washington.edu/browning/beagle/intro-to-vcf.html http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137218/ http://digitheadslabnotebook.blogspot.fr/2013/01/vcf-variant-call-format.html

ADD REPLY • link 10.1 years ago by Pierre Lindenbaum 161k

0

Entering edit mode

Can a file .vcf generate a SNP database?

ADD REPLY • link 10.1 years ago by hudarembang • 0

0

Entering edit mode

what is a "SNP database" a RDMS ? define "generate"

ADD REPLY • link 10.1 years ago by Pierre Lindenbaum 161k

0

Entering edit mode

yes, i will try to become a SNP database. generate == "be processed for". is there a journal / paper related with "snp database and vcf"? I'm sorry, I am still a beginner in learning in bioinformatics.

ADD REPLY • link 10.1 years ago by hudarembang • 0

0

Entering edit mode

ask a new question on biostars please.

ADD REPLY • link 10.1 years ago by Pierre Lindenbaum 161k

score 3 · Answer 1 · 2014-03-12

A variant must have a location in the genome. This location is denoted by the chromosome/contig (#CHROM column) and base position on it (POS column). Note that the position is 5', which is important mostly for indels, since this could otherwise be ambiguous. Have a read through the spec (this is a somewhat outdated version, but the principals are the same).