Fields In The Vcf File
#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?
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Devon Ryan
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hudailkom47 •
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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 Have a read through the spec (this is a somewhat outdated version, but the principals are the same).
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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
Can a file .vcf generate a SNP database?
what is a "SNP database" a RDMS ? define "generate"
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.
ask a new question on biostars please.