HBA phasing problems

[mnfrandre]

Dear Xiao Chen,

Thanks for your good phasing tools!
I was using Paraphase 3.1.1 to call genotypes for HBA genes. Alpha3.7 deletion and anti3.7 genotypes performed well (with hba_del and hba_dup repectively), However genotypes for 4.2 deletion and duplication could not be called. Here is my IGV screenshot:

Apparently, this sample has a HBA2 deletion(4.2 deletion) with breakpoints supported. Any ideas for this problem?

Thank you very much!

[mnfrandre]

Also, attached is my hg39 mapped bam file.
hba4.2del_test.zip

[xiao-chen-xc]

Hi @mnfrandre Paraphase is currently not designed to pick up the 4.2 deletion. I'll see if it's possible to add it into Paraphase. Would you mind re-uploading your bam file? I downloaded it but was not able to unzip it.

[mnfrandre]

hba4.2del_test.hg38.zip

@xiao-chen-xc Many thanks!

[xiao-chen-xc]

This data is very useful. Thanks @mnfrandre! I have added 4.2 deletion and duplication to HBA calling in Paraphase. This will be available in Paraphase Version 3.2, which I plan to release in about 7-10 days.

[mnfrandre]

@xiao-chen-xc Good news! Thanks for your job!

[xiao-chen-xc]

Hi @mnfrandre Version 3.2 is released. Please try it and let me know if anything can be improved.