https://github.com/ekg/hapviz

indel haplotype visualization on the command line from BAM files
https://github.com/ekg/hapviz

Last synced: 4 months ago
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indel haplotype visualization on the command line from BAM files

• Host: GitHub
• URL: https://github.com/ekg/hapviz
• Owner: ekg
• Created: 2011-01-26T22:32:58.000Z (over 13 years ago)
• Default Branch: master
• Last Pushed: 2014-03-12T15:40:43.000Z (over 10 years ago)
• Last Synced: 2024-01-17T03:19:06.755Z (6 months ago)
• Language: C++
• Homepage:
• Size: 203 KB
• Stars: 11
• Watchers: 5
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README

Lists

• repo-5916-awesome-genome-visualization - Hapviz - genome-visualization/hapviz.png) (Text based)
• awesome-genome-visualization - Hapviz

README

        
hapviz: region-bounded haplotype pileup visualization for BAM files

it all happens in the terminal!

    % hapviz --help

    usage: hapviz [options] bam file [... bam file]

    options:

        -b, --bam           bam file to from which to extract reads

                            (may also be specified as positional arguments)

        -r, --region        region from which to extract grouped reads

        -a, --show-all      When visualizing, show all alignments, not just variant ones.

        -f, --reference     FASTA reference against which alignments have been aligned

        -q, --min-base-quality

                            minimum base quality required for all bases in a read

    Displays haplotype groups from the specified region across the BAM files provided as input.

Note: If you list 'stdin' as one of the BAM files, you can pipe BAM directly into hapviz.

This (slightly modified) example output shows how each indel haplotype is

grouped, and the reads from it are aligned to a reference sequence.  Relative

deletions between the reference and reads are replaced by '-'.

17 i:16817:GGCAC

                      16788   CCCAGCACTTCAGGGCTTTAGCTGGGAGGGA-----GGCAGTCCACAGGAATGAATTCATCACT   16862

sample08 31M5I34M              CCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAAT

sample03 30M5I35M               CAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATG

sample02 27M5I38M                 GCACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAAT

sample05 26M5I39M                  CACTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATT

sample05 24M5I41M                    CTTCAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCA

sample07 21M5I44M                       CAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCA

sample07 21M5I44M                       CAGGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCA

sample03 19M5I46M                         GGGCTTTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCACT

sample08 14M5I51M                              TTAGCTGGGAGGGAGGCACGGCAGTCCACAGGAATGAATTCATCACT

--------------------------------------------------------------

1 i:16817:GGCAG

                      16765   GTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGA-----GGCAGTCCACAGG   16829

sample03 52M5I13M             GTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCAGGGCAGTCCACAGG

--------------------------------------------------------------

1 i:16821:T

                      16758   ATACAGGGTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCA-GTC   16823

sample03 63M1I3M3S            ATACAGGGTGCTGCCCTCTCCCCAGCACTTCAGGGCTTTAGCTGGGAGGGAGGCATGTC

--------------------------------------------------------------

Enjoy!

author: erik garrison 

license: free