https://github.com/stuntspt/4pipe4_to_genotyping_array

A script to convert 4Pipe4 SNP output to a genotyping array in FASTA format
https://github.com/stuntspt/4pipe4_to_genotyping_array

Last synced: 12 months ago
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A script to convert 4Pipe4 SNP output to a genotyping array in FASTA format

• Host: GitHub
• URL: https://github.com/stuntspt/4pipe4_to_genotyping_array
• Owner: StuntsPT
• License: gpl-3.0
• Created: 2013-05-14T13:59:44.000Z (almost 13 years ago)
• Default Branch: master
• Last Pushed: 2013-05-14T14:05:17.000Z (almost 13 years ago)
• Last Synced: 2025-01-17T20:45:53.174Z (about 1 year ago)
• Language: Python
• Size: 117 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
#4Pipe4_to_sequenom

###This program will transform a sorted and indexed bam file, plus a FASTA file generated by 4Pipe4 into SNPs and their flanking regions ready for a sequenom Mass Array (c).

###Usage:

    python2 4Pipe4_to_sequenom.py infile.bam infile.fasta variation_treshold(float: 0-1) max_variations(int)

The "infile.bam.bai" has to be in the same directory as the "infile.bam".

###Requirements:

* Python 2.x (tested with 2.7)

* pysam (code.google.com/p/pysam/‎)

###License:

GPLv3.