a question regarding partitions ....

[HMPNK]

Thanks for your software, it was the only one working on my data in reasonable time.
My most urgent question is now:

Do the partioned reads come all from a single haplotype / haploid chromosome?

[bluenote-1577]

Hi @HMPNK,

Glad to know flopp was working.

For each set of reads in the partition file separated by the '#' character, they should come from a single haplotype, yes.

However, switch errors tend to be inevitable. This means that you can be quite confident that reads nearby on the genome come from the same haplotype, but two reads that are a few megabases apart may not come from the same haplotype due to switch errors.