shujiahuang / basevar

This is the official development repository for BaseVar, which call variants for large-scale ultra low-pass (<1.0x) WGS data, especially for NIPT data

Hi there, I'm Shujia Huang! 👋

Hi, I'm Shujia Huang, a bioinformatician, human genome researcher and programmer from China. My primary research interests lie in statistical modeling, bioinformatic method development and data analysis in human genetics and genomics:

• 🔭 I’m currently working at 广州市妇女儿童医疗中心(Guangzhou women and children's medical center)
• 🌱 I’m currently developing bioinformatic algorithms by using Machine learning (including deep learning tech) and Causal inference knowlegde.
• 💬 Ask me about anything here in English or Chinese (Recommend)
• 📫 How to reach me: You can follow my WeChat Official Accounts(微信公众号): helixminer(碱基矿工) or email: [email protected]

basevar's Issues

Too many reads (5000001) in region

Hi, I have two errors in using the software for calling variants of 20,000 bams. The first one is, sometimes it reminds me can not open the index of bam; but I am sure the bam and the corresponding index are all good. The second one is, it reminds me too many reads in some region, and suggests me to reduce --buffer-size or increase --max_reads. Once I increase the max reads to 5000000000, the software still can not work. could you please help me to explain how these errors happen and give me some advisement?

Can you talk about how to use the basevar result for imputation with STITCH?

Can you talk about how to use basevar results for imputation with STITCH?

I read your article, and your safeware is so good.

I want use your software to do some analysis. I see there some VCF files in basevar results. could the VCF files be the input files for STITCH ? How you to use the STITCH with basevar? Can you share the usage? Thanks a lot.

Thanks for your reply.

undefined symbol: hts_utell

I use the commad ""/usr/bin/basevar" -h",but it dosnt work !

return me "undefined symbol: hts_utell"

whole waring:
Traceback (most recent call last):
File "/usr/bin/basevar", line 9, in
load_entry_point('basevar==0.8.0', 'console_scripts', 'basevar')()
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 378, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2566, in load_entry_point
return ep.load()
File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 2260, in load
entry = import(self.module_name, globals(),globals(), ['name'])
File "/usr/lib64/python2.7/site-packages/basevar/runner.py", line 13, in
from caller.executor import BaseTypeRunner
File "basevar/caller/executor.pyx", line 1, in init basevar.caller.executor
"""
File "basevar/io/fasta.pyx", line 8, in init basevar.io.fasta
from basevar.io.openfile import Open
File "basevar/io/openfile.pyx", line 11, in init basevar.io.openfile
from basevar.io.BGZF.bgzf import BGZFile
File "basevar/io/BGZF/bgzf.pyx", line 1, in init basevar.io.BGZF.bgzf
# cython: embedsignature=True
ImportError: /usr/lib64/python2.7/site-packages/basevar/io/htslibWrapper.so: undefined symbol: hts_utell