TypeError: '<' not supported between instances of 'str' and 'int'

[dahaigui]

Got an error when loaded GATK result with PyBSASeq BulksOnly script.

Perform SNP filtering Traceback (most recent call last): File "/data/mg1/chenhx/software/PyBSASeq/BulksOnly/PyBSASeq.py", line 993, in <module> bsaSNPs = snpFiltering(snpRawDF) File "/data/mg1/chenhx/software/PyBSASeq/BulksOnly/PyBSASeq.py", line 112, in snpFiltering df_lowq = df[(df[fb_GQ]<gqValue) | (df[sb_GQ]<gqValue)] File "/data/mg1/chenhx/miniconda3/lib/python3.6/site-packages/pandas/core/ops/common.py", line 65, in new_method return method(self, other) File "/data/mg1/chenhx/miniconda3/lib/python3.6/site-packages/pandas/core/ops/__init__.py", line 370, in wrapper res_values = comparison_op(lvalues, rvalues, op) File "/data/mg1/chenhx/miniconda3/lib/python3.6/site-packages/pandas/core/ops/array_ops.py", line 244, in comparison_op res_values = comp_method_OBJECT_ARRAY(op, lvalues, rvalues) File "/data/mg1/chenhx/miniconda3/lib/python3.6/site-packages/pandas/core/ops/array_ops.py", line 56, in comp_method_OBJECT_ARRAY result = libops.scalar_compare(x.ravel(), y, op) File "pandas/_libs/ops.pyx", line 103, in pandas._libs.ops.scalar_compare TypeError: '<' not supported between instances of 'str' and 'int'

[dblhlx]

Sorry for the late replay. I didn't receive any email notification of this issue from github.

Would you please send me a small subset of your data?

[dblhlx]

@dahaigui, what variable type is the GQ value in your dataset. It is float in my dataset.

[dblhlx]

I'll close this issue since I haven't heard from you for a long time. Please reopen it if you still have this problem. Please attach a thousand rows of your data in case you reopen this issue.