extracting pruned bam file

[aleksandrabliznina]

Hello!

Thank you so much for your tool! I found it promising for some of my complicated genomes.

I was wondering if there is a way to extract pruned bam file so it can be used for other things?

Best regards,
Alex

[wangyibin]

Hi Alex,

Thanks for your interest in C-Phasing.

Yes, you can extract the pruned BAM using the pruning table generated by Kprune.

New version of cphasing-rs download from "https://drive.google.com/file/d/1_j2KqQLJr9Xs2xTbKpJYySfCpnpE-nqp/view?usp=drive_link"

cat cphasing_output/3.hyperpartition/kprune_wrkdir/*prune.table > whole.prune.table
cphasing-rs bam-prune --bam input.bam -p whole.prune.table -o prune.bam

Alternatively, if you are working with pairs files, you can also do:

cphasing-rs pairs-prune -i input.pairs.pqs -p whole.prune.table -o prune.pairs.pqs
cphasing-rs pairs2bam prune.pairs.pqs -o prune.pairs.bam

Best,
Yibin

[aleksandrabliznina]

Hi Yibin,

Thank you for your reply! Unfortunately, I do not have access to the drive you shared. And downloading the latest version from github, I do not see the bam-prune or pairs-prune commands.

The only commands available are: cphasing-rs prune and cphasing-rs kprune which both require <ALLELETABLE> and <CONTACTS> files, which I am not sure what they exactly correspond to.

The problem is that I can see cphasing grouping contigs into right chromosome groups, but within assembled "chromosomes", there are still quite a lot of misassemblies. I would like to be able to extract the pruned bam file of reads mapped to the contigs and feed it to some other scaffolders, like YaHS or something. Do you have any suggestions on that?

Best regards,
Alex