Hello. I have some VCF files which I will be working with. Today I came across a tool named VCF Tools and it seems like it might be useful. However, before I download and install it, I was wondering if it will be able to answer all of the following case scenarios or should I build my own program to parse my files?
Case Scenario 1:
All known (have an RS id) polymorphic positions for sample IDs starting with P0048* with AF<0.10.
Case Scenario 2:
All unknown polymorphic positions for sample IDs starting with P0048* with AF<0.10.
Case Scenario 3:
All known (have an RS id) polymorphic positions for sample IDs starting with P0048* with AF<0.10. Report the genotypes for all individuals in the family that have a coverage for those positions greater than 20 (i.e. DP >20) for individuals with DP <20 replace genotype with ./.
Thanks!
Case Scenario 1:
All known (have an RS id) polymorphic positions for sample IDs starting with P0048* with AF<0.10.
Case Scenario 2:
All unknown polymorphic positions for sample IDs starting with P0048* with AF<0.10.
Case Scenario 3:
All known (have an RS id) polymorphic positions for sample IDs starting with P0048* with AF<0.10. Report the genotypes for all individuals in the family that have a coverage for those positions greater than 20 (i.e. DP >20) for individuals with DP <20 replace genotype with ./.
Thanks!