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Understanding position of indels within VCF File [HaplotypeCaller]
Given the deletion-call of:
I 308 . CT C 12492.73
What is the POS value (308) specifically denoting? Is it specifying the position at which the T would otherwise have been found in the reference if it was present? Is it the coordinate of the 'C'?
Secondly, for more complex deletions/insertions, such as:
I 287 . C CTG 16225.73
How is the POS value now determined given that more than 1 letter has changed?
Thirdly, is there a way to obtain start + stop coordinates for indels from GATK rather than just a single position?