Haploid data in VCFTools
0
1
Entering edit mode
5.8 years ago


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 vcftools haploid SNP • 2.5k views
ADD COMMENT

Login before adding your answer.

Traffic: 2988 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6