chunk start/stop points in [output].bfs.gz don't match those in -bed [file name]

[sophiesmart]

Hello,

I'm hoping someone can help me. I've sucessully run gwas-pw but in persuing downstream analyses I've noticed that the genomic regions in my output file don't correspond to the input file (I'm using Berisa2015_EURbreakpoints_chr23.bed as recommended).

For example, in [output].bfs.gz chunk 80 on chrmosome 1 runs from 159914924 to 162344102
chunk NSNP chr st sp
80 3553 chr1 159914924 162344102

but in Berisa2015_EURbreakpoints_chr23.bed chunk 80 runs from 158027412 to 159913048
chr1 158027412 159913048

the exact start and stop positions in [output].bfs.gz are not explicity listed in Berisa2015_EURbreakpoints_chr23.bed. In this case, the chunk in [output].bfs.gz closely resembles the one in Berisa2015_EURbreakpoints_chr23.bed but for other output chunks they do not.

For example, in [output].bfs.gz chunk 1602 on chrmosome 19 runs from 47158591 to 49253389
chunk NSNP chr st sp
1602 2142 chr19 47158591 49253389

but in Berisa2015_EURbreakpoints_chr23.bed chunk 1602 runs from 34262952 to 36469295
chr19 34262952 36469295

Can anyone explain what is happening "under the hood" to result in this shift?