search

Illumina / manta

Structural variant and indel caller for mapped sequencing data
GNU General Public License v3.0
404 stars 154 forks source link

Split and spanning reads #285

Open dmaziec opened 2 years ago

dmaziec commented 2 years ago

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 commented 1 year ago

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