Accept existing mapping results

[xiekunwhy]

Hi,

Can you add some option to accept existing read mapping results like bam file generated from HapHiC suggested bwa mem pipeline or HiC-Pro pipeline (although HiC-Pro bam not so suitable for phasing genome anchoring, but it is excellent for haploid genome anchoring.)

Best,
Kun

[wangyibin]

Hi,
Thank you for your advice. We will be adapting bam file input in the next minor release, and now we recommend that users use existing bam files in the following way:

cphasing bam2pairs sample.nsorted.bam -o sample.pairs.gz 

Note: the input bam file should not be sorted by the coordinates.

Best,
Kun

[xiekunwhy]

Thank you for your reply, I will try bam2pairs.