Creating haplotypes from vcf/NGS data

[pettervikman]

Hi

I'm trying to create haplotypes from my NGS data and my current choice of tool is haploviewer. I have however not been able to use the family structure that I have in my data set. So to sum up what I've done:

Created the .ped and .info file. Both of them work if I set all the parents to 0 in the .ped file, having the parents with correct numbers doesn't work. The family is relatively large, 23 members with NGS data from three generations and another 12 "dummies" i.e parents where I lack NGS data so all their genotypes are 0 0.

So since it works with setting all parents as 0 0 I know that the genotypes are corrects and sex/affliction status/family name works. There are no sibling/cousin marriages but several individuals share parents. I have pasted a copy of the first columns for viewing at the end.

If I could get help either with getting haploviewer to work or any other program that can work with family structures and lots of data (up to 10-15.000 variants and 50-60 individuals) and in a perfect world able to do associations with permutations I'd be much obliged. The data is both from whole exom seq and from targeted seq with variants much closer together.

Sincerely

/Petter

FAM1 1238 0 0 1 2 1 3
FAM1 1240 0 0 2 1 3 3
FAM1 1245 0 0 1 2 1 3
FAM1 1246 0 0 1 1 3 3
FAM1 1248 0 0 1 2 1 3
FAM1 1251 0 0 1 1 3 3
FAM1 1255 0 0 1 1 1 3
FAM1 1256 0 0 2 1 1 3
FAM1 1257 0 0 1 1 3 3
FAM1 1258 0 0 2 1 1 3
FAM1 1259 0 0 2 1 1 3
FAM1 1260 0 0 1 1 3 3
FAM1 1261 0 0 2 2 1 3
FAM1 2409 0 0 1 2 1 3
FAM1 2411 0 0 2 1 1 1
FAM1 482 0 0 1 1 1 3
FAM1 596 0 0 2 1 3 3
FAM1 598 0 0 1 2 1 3
FAM1 627 0 0 1 1 1 3
FAM1 631 0 0 1 2 1 3
FAM1 865 0 0 2 1 3 3
FAM1 956 0 0 1 1 1 3
FAM1 957 0 0 2 2 3 3
FAM1 1 0 0 2 1 0 0
FAM1 2 0 0 1 1 0 0
FAM1 7 0 0 1 2 0 0
FAM1 8 0 0 2 1 0 0
FAM1 10 0 0 2 0 0 0
FAM1 18 0 0 2 0 0 0
FAM1 19 0 0 1 1 0 0
FAM1 20 0 0 2 0 0 0
FAM1 29 0 0 2 0 0 0
FAM1 32 0 0 1 0 0 0
FAM1 44 0 0 1 0 0 0
FAM1 45 0 0 2 2 0 0