Alisa
Alisa
Hi Lucas and John, Thank you so much for your input. I’m currently trying to figure out what’s happening… with different references..! Kind regards, Alisa
Hey, sorry to reopen the issue. I called variants against HLA class II genes region for HG003 using HG003_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed and have very low precision values :( probably I am doing...
Hi @kishwarshafin, I think the problem is that it is HLA... I did probably very stupid reference-guided alignement and actually received lower coverage for the whole HLA, so starting from...
> So do you think these are misassemblies? yes, because one haplotype is empty and another one has two contigs :(
or there is a duplication 
so any ideas why this happens? I have tweaked many parameters, but in the end when the problem is resolved for 1 sample, it appears in another. I see haplotype...
strange, but the *first_pass.summary.csv is produced anyway
I think it is an issue with python, I had to downgrade to python=3.9 for my environment. Hope that helps. @cjw85 are you planning to upgrade for python>3.9 or is...