How variant locations work when there is an INDEL around?

Question

[magnolia]

Hi everyone,

I'm wondering how SNPs are presented when there is an INDEL before them. For example, if there is a deletion (ATTA) at 12345, the next SNP T --> C starts at 12349 or at 12346?

Thanks a lot in advance!

[Pierre Lindenbaum]

if they are _phased_, gatk might use a spanning deletion * : https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-

[magnolia]

Thank you so much! From the example they give, I understand that it's impossible to have deletion and also the SNP homozygously. So if deletion is 1/1 and SNP is also 1/1 (separate rows), something definitely wrong there. Right?