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Circle Map Realign manual
In this sub-wiki we will explain the default parameter settings of Circle-Map Realign. Moreover, for those parameters that might have a strong impact on the output when modified, we will advise on how to tune and optimize them to obtain reliable results when you use the software under non-standard approaches.
This section explains the mandatory input files to execute Circle-Map Realign. This are the required arguments
-i Input: bam file containing the reads extracted by ReadExtractor
This argument must take as input a coordinate sorted BAM file that contains all the reads indicating circular DNA like structural variation. The BAM file must be indexed with SAMtools index. Circle-Map will use this file to identify split and discordant reads and detect the circular DNA, thus, it is the main input file. Ideally, it should be the output of Circle-Map ReadExtractor. However, the software should still give reliable results (warning: we have not tested this) with a regular sorted BAM file at the expense of a longer runtime.
-qbam Input: query name sorted bam file
This argument must take as input a queryname sorted BAM file containing all the raw BWA MEM generated alignments to the reference genome. Circle-Map will use this file to estimate the insert size distribution, which is then used to construct the realignment graph.
-fasta Input: Reference genome fasta file
This argument must take as input the reference genome in FASTA format. Furthermore, the reference genome must be indexed with SAMtools faidx. This file is required by Circle-Map to sample the sequence of the graph interval to attempt the realignment of the soft-clipped reads.
-o Output filename
This argument must take as input the name (e.g my_beautiful_circles.bed) of the output file you will create with Circle-Map. It is not a strict requirement to provide this argument. The software will work if you do not provide it, creating a file called "circle_" + name of the BAM file used as main input. Yet, we strongly encourage to provide a file name as Circle-Map will overwrite a file that contains the name "circle_" + "name of the BAM" in your system.
-n , --nhits Number of realignment attempts. Default: 10
This argument must take as input an integer indicating the the number of suboptimal alignments to look for before giving up the search. The default value is set to 10 as as it will look to a enough number of suboptimal hits without substantially losing speed.
-p , --cut_off Probability cut-off for considering a soft-clipped as realigned: Default: 0.99
This argument must take as input a float indicating the realignment probability cut-off for the soft-clipped reads. Unless you have a very good reason to modify this parameter, we suggest you always run your analysis using the default setting.
-m , --min_sc Minimum soft-clipped length to attempt the realignment. Default: 5
This argument must take as input an integer indicating the minimum length required for Circle-Map to try to realign a soft-clipped read. If you increase the value Circle-Map will run faster, but the sensitivity will be decreased.
-g , --gap_open Gap open penalty in the position specific scoring matrix. Default: 5
This argument must take as input an integer indicating gap open penalty to score realignments.
-e , --gap_ext Gap extension penalty in the position specific scoring matrix. Default: 1
This argument must take as input an integer indicating gap open penalty to score realignments.
-q , --mapq Minimum mapping quality allowed in the supplementary alignments. Default: 20
This argument must take as input an integer indicating to minimum mapping quality required for the BWA MEM flagged supplementary alignments te be considered as circular DNA support. Unless you have a very good reason to modify this parameter, we suggest you always run your analysis using the default setting.
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-Q , --split_quality Minium split score to output an interval. Default (0.0)
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-R, --remap_splits Remap probabilistacally bwa-mem split reads
UNDER DEVELOPMENT