Question: Vcf For Homozygous Variety Snp
1
gravatar for ric
5.8 years ago by
ric100
ric100 wrote:

Hi, I tried to understand VCF 4 for homozygous variety SNPs, but I do not know how to convert the following genotypes to VCF:

    genotypes:
    - variety1 = 2*G (variety1 has two G's at locus position)
    - variety2 = 3*A (variety2 has two A's at locus position)
    allele       A/G

This is the beginning of the VCF file, but I stucked with above genotypes

    #CHROM - X8r  
    POS     391
    ID      X8r0000001
    REF     G
    ALT     A
    QUAL    2
    FILTER  .
    INFO    DP=5
    FORMAT

How to create a VCF 4 file for the above homozygous variety SNP?

Thank you in advance.

vcf snps variant snp • 1.7k views
ADD COMMENTlink modified 5.8 years ago by Giovanni M Dall'Olio26k • written 5.8 years ago by ric100

Have you looked here? http://www.1000genomes.org/node/101

For variety1 do you need something like this?

X8r 391 X8r0000001 G A 2 . DP=5 0/0

This wouldn't be homework, would it?

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by Alex Paciorkowski3.3k
1
gravatar for ric
5.8 years ago by
ric100
ric100 wrote:

Thank you, I just try to understand the format. I found also this http://seqanswers.com/forums/showpost.php?p=68687&postcount=3 definition

    genotypes:
    - variety1 = 15*G (variety1 has two G's at locus position) J
    - variety2 = 1*C (variety2 has two A's at locus position) M1
    - variety3 = 1*T (variety3 has two A's at locus position) M2
    allele       C/G/T

X8r 1 X8r0000001 G C,T 2 . DP=17 GT:DP 0/0:15 1/1:1 2/2:1

Would the above line a correct VCF 4 line?

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by ric100

This looks correct

You can check your formatting with the validator from vcf-tools http://vcftools.sourceforge.net/perl_module.html#vcf-validator

ADD REPLYlink written 5.8 years ago by Laura1.7k
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