If the alternate allele in the variant is not symbolic, & SVLEN is integral but not equal to len(ALT) - len(REF), set it to this value.
Fix END value for precise variants
If a variant is flagged as precise (using IMPRECISE=0), & END is an integer nut not equal to POS + len(REF) - 1, set it to this value.
Removal of duplicates in ID
The fix is to keep the first duplicated ID, and remove all consequent ones.
Removal of duplicates or 0's in FILTER
The fix is to remove all 0's (if present) and keep the first duplicate filter, & remove the consequent ones.
Removal of duplicates in INFO
The fix here is :
i) remove all the duplicate fields, if there are different values for the same key (we cannot give preference to any particular field)
ii) keep first and remove all consequent occurrences of a field if for the key, all the duplicate fields have the same value
Removal of duplicates in FORMAT
The fix is:
i) remove all duplicate fields from the format and sample(s) columns, if there are different values in one or more of the samples
ii) keep first and remove all consequent occurrences of a field from format and sample(s) if each sample has the same value for that field
The fixes added are :
Fix SVLEN value for non-symbolic ALTs
If the alternate allele in the variant is not symbolic, & SVLEN is integral but not equal to
len(ALT) - len(REF), set it to this value.Fix END value for precise variants
If a variant is flagged as precise (using IMPRECISE=0), & END is an integer nut not equal to
POS + len(REF) - 1, set it to this value.Removal of duplicates in ID
The fix is to keep the first duplicated ID, and remove all consequent ones.
Removal of duplicates or
0's in FILTERThe fix is to remove all 0's (if present) and keep the first duplicate filter, & remove the consequent ones.
Removal of duplicates in INFO
The fix here is : i) remove all the duplicate fields, if there are different values for the same key (we cannot give preference to any particular field) ii) keep first and remove all consequent occurrences of a field if for the key, all the duplicate fields have the same value
Removal of duplicates in FORMAT
The fix is: i) remove all duplicate fields from the format and sample(s) columns, if there are different values in one or more of the samples ii) keep first and remove all consequent occurrences of a field from format and sample(s) if each sample has the same value for that field