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Query Mutated Reads from a Bam

License: MIT License

Python 90.43% Julia 4.89% Shell 4.68%

accurate-frequency post-dedup unique-reads

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ylxdzsw realityjunky bgistone haokuo guanminxiao wangdi2014 shannondaddy

mrbam's Issues

how to judge whether a read to support an INDEL from VCF ?

HI ,
what's the condition of the read to support INDEL(deletion or insertion) from VCF ??
could you please show your code ?
thank you!

A question about

TypeError: 'NoneType' object is not iterable

I have encountered an error while running MrBam. The error is "TypeError: 'NoneType' object is not iterable" . please help me out to fix it
Thanks!

Handle the issue when run with python2

Since the default python version is 2.7, this tool should handle the error caused by using default python 2.7, and then suggest the user to use python3

Error while performing MrBam with Python 3.6.8

I have some issue when running MrBam.

line 31, in anno
    pos =int(line[1]) - 1
ValueError: invalid literal for int() with base 10: 'Start'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "Mrbam.py", line 86, in <module>
    anno(o)
  File "/home/rico/Downloads/MrBam-master/MrBam/anno.py", line 33, in anno
    raise Exception("vcf header should be expluded", o.query)
Exception: ('vcf header should be expluded', '/home/rico/Downloads/TagSequencing.snp.hg19_multianno.txt')

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