Part 2:  Using the pedigree and recessive inheritance to filter SNPs.

1. Selecting the heterozygous SNPs from the parents.
2. Selecting the homozygous SNPs from the affected children.
3. Finding the SNPs in common for all 4 sets above.
4. Finding the homozygous SNPs in the unaffected child.
5. Subtracting the SNPs from step 4 from those in step 3.

Note: If using your own data with disease SNPs already included upload the pgSnp, VCF, or masterVar files into Galaxy using the URL method as shown in part 1 (or the ftp method). For VCF or masterVar files there are tools to convert to pgSnp format under Convert formats.