Entering edit mode
9.1 years ago
xinhui.wang
▴
550
Dear all,
I am generating ped file from VCF files with VCF tools with the following tools
vcftools --vcf test.vcf --remove-indels --plink --chr Chr1 --out test
Everything worked very well except that I have 0 when I had Homozygous.
For example
Sample_10B Sample_10B 0 0 0 0 0 0 0 0 0 0
Sample_11B Sample_11B 0 0 0 0 0 0 0 0 0 0
Sample_12B Sample_12B 0 0 0 0 0 0 0 0 0 0
Sample_13C Sample_13C 0 0 0 0 0 0 0 0 T C
Sample_14C Sample_14C 0 0 0 0 C T T T C C
Sample_15C Sample_15C 0 0 0 0 0 0 0 0 C C
Sample_16C Sample_16C 0 0 0 0 0 0 0 0 C C
Sample_17C Sample_17C 0 0 0 0 C T C T C C
Sample_18C Sample_18C 0 0 0 0 0 0 0 0 C C
Sample_19D Sample_19D 0 0 0 0 C T C T T C
Sample_1A Sample_1A 0 0 0 0 0 0 0 0 0 0
Sample_20D Sample_20D 0 0 0 0 C T C T C C
Sample_21D Sample_21D 0 0 0 0 0 0 0 0 0 0
Sample_22D Sample_22D 0 0 0 0 C T C T T C
Sample_23D Sample_23D 0 0 0 0 0 0 0 0 C C
Sample_24D Sample_24D 0 0 0 0 0 0 0 0 T C
Sample_2A Sample_2A 0 0 0 0 T T T T C C
Sample_3A Sample_3A 0 0 0 0 T T T T T C
In 7th and 8th column, the 0 should be reference allele as C. I do not think I am the unique one who had this problem, could any one help me with this point?
Thanks and with best regards,
Xinhui
