Question: Haploid data in VCFTools
1
gravatar for whiteeagle115
22 months ago by
Brazil
whiteeagle11510 wrote:


Hi everyone!

I'm having problens on using haploid data (from VCF format) in VCFtools. First, I have a merged VCF with 9 samples and I need to do some statisthical analyses (like pi, Tajima D and LD).

I just see the mailing list from VCftools-help and it's seeing to be just to change the alleles 1 to 1|. It's working until I see the result. 

My data is like that:

Chromosome_1.1    6273    .    C    G    870.77    PASS    AC=1;AF=1.00;AN=1;DP=23;Dels=0.00;EFF=INTERGENIC(MODIFIER||||||||||1);FS=0.000;HaplotypeScore=0.9665;MLEAC=2;MLEAF=1.00;MQ=41.74;MQ0=0;QD=25.00;set=variant6    GT    ./.    ./.    ./.    ./.    1|.    ./.    ./.    ./.    ./.
Chromosome_1.1    9122    .    C    G    774.77    PASS    AC=1;AF=1.00;AN=1;DP=21;Dels=0.00;EFF=INTERGENIC(MODIFIER||||||||||1);FS=0.000;HaplotypeScore=1.9850;MLEAC=2;MLEAF=1.00;MQ=41.72;MQ0=0;QD=27.36;set=variant9    GT    ./.    ./.    ./.    ./.    ./.    ./.    ./.    ./.    1|.
Chromosome_1.1    11188    .    G    A    734.77    PASS    AC=1;AF=1.00;AN=1;DP=21;Dels=0.00;EFF=INTERGENIC(MODIFIER||||||||||1);FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=41.72;MQ0=0;QD=34.99;set=variant5    GT    ./.    ./.    ./.    ./.    ./.    1|.    ./.    ./.    ./.

 

For exemple, in command:

vcftools --vcf Test_Vcftools.vcf --TajimaD 1000 --out out

 

The result is just a empty doc with only the reader:

CHROM   BIN_START       N_SNPS  TajimaD

Thanks for any help!

 

 

 

 

 

 

 

myposts snp vcftools haploid • 860 views
ADD COMMENTlink written 22 months ago by whiteeagle11510
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