I want to remove all rows with a minor repeating count less than 30% compared to the major repeating count from my table. The values of a col(starting col 2) can assume is A,T,G,C and N. Each row has at least 2 values and at most 4 repeating values(out of ATGC).
N is considered a missing value and shouldn't be considered.
These are the rules for filtering.
Consider the row which has a count of 4 for Ts and 1 for As (starting col 2). S10_14113025 T T T A T
If the count of the minor repeating value is less than 30% of the major repeating value, delete the row.
So count(A)/count(T)=1/4=25% < 30%...this row should be removed.
Consider the row with 2 Ts, and 1 A. S10_14113025 T N N A T
Ignoring the Ns, the minor frequency is
count(A)/count(T)=1/2=50% > 30% ....this row should NOT be removed.
Consider the row with more than 2 values (3 in this case as in G,C,A). S10_14113072 G C A G N this row should NOT be removed,nothing needs to be calculated.
We only need to filter rows having biallelic nature (exactly two values excluding N).
The rows with more than two values are biologically significant and cant be filtered out.
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