diff --git a/docs/format.md b/docs/format.md index 6ac5a4b..56a3943 100644 --- a/docs/format.md +++ b/docs/format.md @@ -1,8 +1,12 @@ # The Population Syntenty File Format (PSF) + Updated to v0.3 file format 2024-09-11 Leon Rauschning + Updated to v0.2 file format 2024-05-22 Leon Rauschning + Created 2022-05-11 Leon Rauschning + ## Premise Finding synteny in multiple genomes at once presents a new way of working with the genomes of a population. To represent this novel kind of information, a new file format is needed; at the same time, as much compatibility as possible should be maintained with tools built for pairwise genome comparisons. @@ -31,7 +35,7 @@ To provide full compatibility with BED format, optionally even these annotations CIGAR strings are shortened using [...] \#CHR|START|END|ANN|REF|CHR|START|END|c24|eri|ler|sha ---- +----------------------------------------------------- Chr1|124|530|MERASYN1|ref|.|.|.|.|Chr1:513-919,53=1X11=1X29=1X33=1X16=1X5=1X34=1X190=1X5=1X22=|.|. Chr1|531|1084|MERASYN2|ref|.|.|.|.|Chr1:920-1458,44=1X27=1X94=1X12=1X43=1X136=1X133=15D26=1X4=1X2=1X3=1X5=|.|Chr1:1581-2126,44=1X21=1X5=1X22=1X71=1X12=1X43=1X136=1X173=8D1=1X8=1X Chr1|1090|17001|CORESYN1|ref|.|.|.|Chr1:13-15966,1464=1X[...]|Chr1:1464-17369,1=2X[...]|Chr1:6-15923,5235=1I2344=[...]|Chr1:2132-18108,3=5I50=1X1=4D[...]