The file resources/normalize_vcf.sh doesn't correctly normalize multi-allelic variants.
Suggested change :
bcftools norm \
-m -both \
-d exact \
-f "${REF}" \
--check-ref ws \
--targets "${TARGETS}" | \
Check example:
2 136592357 . CAAAAAAA C,CAAAAAAAAAAAA
The second variant should be normalized as C>CAAAAA
The file resources/normalize_vcf.sh doesn't correctly normalize multi-allelic variants.
Suggested change :
Check example:
2 136592357 . CAAAAAAA C,CAAAAAAAAAAAAThe second variant should be normalized as C>CAAAAA