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Files format

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Darren J. Lin edited this page Nov 23, 2020 · 2 revisions

Required inputs

  1. Reference sequence (FASTA) and index file (FAI).
  2. Mako configuration file.

Mako outputs

Graph nodes file

sampleName.superitems.txt: This file can be found under the working directory. Each record indicates a node in the graph, where each node has 19 columns of information (see table below). File headings

Detected events

sampleName.mako.sites.txt: Mako detect SVs. Additional information of each record can be found in the file heading.

Example of Mako's detection:

chr1	16088762	16089878	ARP_Self;Split	cxs=12;DEL,16088762-16089600,sa=3,rp=0;16089413-16089601,sa=6,rp=0;INV,16088762-16089878,sa=0,rp=10	ARP_RR,ARP_FF,MS,SM,MS,ARP_RR	0+13-,51+0-,9+13-,6+6-,3+4-,0+10-

In this example, Mako score the complexity of this event as 'cxs=12'. Moreover, Mako identifies three internal connections '16088762-16089600,sa=3,rp=0',16089413-16089601,sa=6,rp=0' and '16088762-16089878,sa=0,rp=10', where each connection is provided with support information. Additionally, 'ARP_RR,ARP_FF,MS,SM,MS,ARP_RR' is nodes type in the detected subgraph.

Node types

ARP_RR, ARP_FF and ARP_RF indicating read-pairs of incorrect orientation.

ARP_LARGE and ARP_SMALL indicating read-pairs of abnormal insert sizes.

MS, SM and etc. were derived from CIGAR string of a read.

BNDs

sampleName.mako.BNDs.txt: Break-ends are not able to involve in the current graph, including inter-chromosomes. This will be optimized in our next update such that some inter- or intra-chromosome translocation involved events can be better detected.

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