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?

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

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.

Dear author, hello！
Can I find out if BaseVar supports the use of GPU and how to configure and use GPU.