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Position of Indel event based on the REF
How do I know based on the REF and ALT column of a VCF file the actual position where an indel event happened?
I usually see an event that occur in the 2nd base. For example,
GGCGTGGCGT G,GCGCGTGGCGT --deletion; insertion of "C"
ATTT A,ATT --deletions
But I saw a VCF format documentation(http://samtools.github.io/hts-specs/VCFv4.2.pdf) allowing a different case:
GTC G,GTCT --deletion; insertion of "T" at the end
How is UnifiedGenotyper formatting the indels? Does it differ
from the one used in the 1000Genome Project? Thank you!