https://github.com/mehelmy/pileup_consensus

Script that takes samtools pileup output and write consensus fasta file as output.
https://github.com/mehelmy/pileup_consensus

Last synced: 3 months ago
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Script that takes samtools pileup output and write consensus fasta file as output.

• Host: GitHub
• URL: https://github.com/mehelmy/pileup_consensus
• Owner: MeHelmy
• License: mit
• Created: 2019-06-27T22:05:07.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2020-04-23T08:05:05.000Z (about 5 years ago)
• Last Synced: 2025-03-23T21:45:48.390Z (3 months ago)
• Language: Python
• Size: 16.6 KB
• Stars: 4
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# pileup consensus

~~~

Script takes samtools pileup output and write consensus fasta file as output.

usage: pileup_consensus.py [-h] [-v] [-n BASE] [-r READS] [input] [output]

Produce consensus fatsa from samtools pileup output

positional arguments:

  input                 pileup file 

  output                Output file if no file result will be directed to

                        stander output

optional arguments:

  -h, --help            show this help message and exit

  -v, --version         show program's version number and exit

  -n BASE, --base BASE  Number of bases in line. (default: 80)

  -r READS, --reads READS

                        Minimum number of reads to accept nucleotide as a

                        variant. (default: 2)

pileup_consensus.py version 0.01. use command -h for info.

~~~