Snps annotation using snpEff or R

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7.9 years ago

mms140130 ▴ 60

I have the following data in VCF format I want to annotate the Snps I have in this file What is the code needed in snpEff or the code by R

#CHROM  POS ID  
    chr7    78599583    rs987435
    chr15   33395779    rs345783
    chr1    189807684   rs955894
    chr20   33907909    rs6088791
    chr12   75664046    rs11180435
    chr1    218890658   rs17571465
    chr4    127630276   rs17011450
    chr6    90919465    rs6919430
    chr16   5748791     rs2342723

SNP gene R • 3.8k views

ADD COMMENT • link updated 7.9 years ago by zx8754 12k • written 7.9 years ago by mms140130 ▴ 60

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snpEff is very well documented, please read and try some example: http://snpeff.sourceforge.net/SnpEff_manual.html

ADD REPLY • link 7.9 years ago by zx8754 12k

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I answered question like this here A: What is the best method to map snps called using GATK to corresponding genes?

ADD REPLY • link 7.9 years ago by Medhat 9.8k

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