{"repo":"jonas-fuchs/BAMdash","free":true,"listed":false,"github":"https://github.com/jonas-fuchs/BAMdash","clone":"git clone https://github.com/jonas-fuchs/BAMdash.git","description":"create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks","language":"Python","stars":58,"topics":["bam-files","bed-files","coverage-report","dashboard","genbank-files","interactive","plotly","vcf-files"],"license":"GPL-3.0","category":"dashboards-admin","readme_excerpt":"Overview BAMdash lets you create interactive coverage plots from your bam file with plotly - requires only a .bam , .bai and the reference id to which the reads where mapped - create a interactive html for data exploration - create a static image ( jpg , png , pdf , svg ) ready for publication - add additional tracks (supported: .vcf , .gb , .bed ) - annotate tracks with additional information - export annoated track data as tabular files ( .bed , .vcf ) or json ( .gb ) - developed for viral genomics - customize all plotting parameters Feel free to report any bugs or request new features as issues! Automatic annotation BAMdash automatically computes serveral statistics: - if -bs is 1 it computes the mean over the bin size in the coverage plot - for each track it computes recovery and mean coverage (set -c for the min coverage) for each element in the track - if a .vcf is provided it annotates TRANSITION / TRANSVERSION and type of exchange ( SNP , DEL , INS ) If a .gb and .vcf is provided BAMdash computes if the mutations could have been caused by APOBEC deamination. Moreover, it annotates the aminoacid exchange and the effect in the CDS (inspired by but not as powerful as snpeff). SNP and INDEL vcf annotation supports: - START LOST : INDEL or SNP start at the CDS and result in a start loss - STOP LOST : INDEL or SNP result in the loss of the stop codon - STOP GAINED : INDEL or SNP result in an additional stop codon - SYN : SNP does not lead to an amino acid change - NON-SYN :","default_branch":null,"files":null,"tree":[],"storefront":"/r/jonas-fuchs","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/jonas-fuchs/BAMdash/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}