Question: Fields In The Vcf File
0
gravatar for hudailkom47
4.4 years ago by
hudailkom470 wrote:
#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?

vcf snp • 1.9k views
ADD COMMENTlink modified 4.4 years ago by Devon Ryan81k • written 4.4 years ago by hudailkom470

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 REPLYlink written 4.4 years ago by Pierre Lindenbaum110k

Can a file .vcf generate a SNP database?

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by hudarembang0

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

ADD REPLYlink written 4.4 years ago by Pierre Lindenbaum110k

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 REPLYlink written 4.4 years ago by hudarembang0

ask a new question on biostars please.

ADD REPLYlink written 4.4 years ago by Pierre Lindenbaum110k
3
gravatar for Devon Ryan
4.4 years ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

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 Have a read through the spec (this is a somewhat outdated version, but the principals are the same).

ADD COMMENTlink written 4.4 years ago by Devon Ryan81k
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