Entering edit mode
8.2 years ago
whiteeagle115
▴
10
Hi everyone!
I'm having problems on using haploid data (from VCF format) in VCFtools. First, I have a merged VCF with 9 samples and I need to do some statistical 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 example, 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!