Split and spanning reads

[dmaziec]

Hello,

In the VCF file, tags for spanning and split reads store the information about the support for the alternative and reference alleles.

##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999">

Could you explain what reads for the ref and alt alleles are in terms of spanning and split reads? How to interpret these values?

Thank you,
Dominika

[lichennan123]

Not sure if this has been addressed or not. But I do have the same question. I wonder whether PR and SR overlaps in some cases and if so, how would I know the total reference and alternate-supporting alleles from PR/SR info? Thank you!

Chennan