Using exome data for IBD analysis

[Scotch]

Does anyone have any experience using exome data to perform Identity-By-Descent analysis? Are there any special tricks or filters that one needs to apply to the data? I ask, because when I run the analysis on my data (see below for details), it shows that each sample is 150-190% related to itself, which is obviously inflated.

(1) start with vcf file
(2) convert vcf file to ped/map using vcftools
(3) download hapmap CEU 60 founders from plink website and filter out any SNPs that are not in the test dataset and in hapmap.
(4) pruned for LD at r2 = 0.2 using --indep-pairwise 50 5 0.2 in plink (actually makes no difference to the results)
(4) run --genome in plink. I've also used gatc software, but get the same results.

All suggestions welcome and many thanks in advance.

[husamia]

I have used the algorithm (http://compbio.charite.de/index.php/ibd2.html) to obtain genomic intervals but I don't know what is a good cutoff and if its helpful.

[bpetersen]

I've also been wanting to try the above script for exome data, but I can't get their script for converting vcf to their ibs format to work on vcf files generated by samtools. How did you get it to work? Do you maybe have a script you would share? Thanks in advance!

[2007lab]

bump! same question as bpetersen.