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 <erik.garrison@bc.edu>
license: free