annotate README.rst @ 3:90c9eb133c86

More integer checking fixes.

1 This repository contains the **Naive Variant Caller** tool.
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5 **What it does**
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7 This tool is a naive variant caller that processes aligned sequencing reads from the BAM format and produces a VCF file containing per position variant calls. This tool allows multiple BAM files to be provided as input and utilizes read group information to make calls for individual samples. 
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9 User configurable options allow filtering reads that do not pass mapping or base quality thresholds and minimum per base read depth; user's can also specify the ploidy and whether to consider each strand separately. 
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11 In addition to calling alternate alleles based upon simple ratios of nucleotides at a position, per base nucleotide counts are also provided. A custom tag, NC, is used within the Genotype fields. The NC field is a comma-separated listing of nucleotide counts in the form of <nucleotide>=<count>, where a plus or minus character is prepended to indicate strand, if the strandedness option was specified.
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16 **Inputs**
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18 Accepts one or more BAM input files and a reference genome from the built-in list or from a FASTA file in your history.
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21 **Outputs**
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23 The output is in VCF format.
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25 Example VCF output line, without reporting by strand:
26     ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:A=9,C=5,T=9629,G=15,``
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28 Example VCF output line, when reporting by strand:
29     ``chrM	16029	.	T	G,A,C	.	.	AC=15,9,5;AF=0.00155311658729,0.000931869952371,0.000517705529095	GT:AC:AF:NC	0/0:15,9,5:0.00155311658729,0.000931869952371,0.000517705529095:+T=3972,-A=9,-C=5,-T=5657,-G=15,``
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31 **Options**
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33 Reference Genome:
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35     Ensure that you have selected the correct reference genome, either from the list of built-in genomes or by selecting the corresponding FASTA file from your history.
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37 Restrict to regions:
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39     You can specify any number of regions on which you would like to receive results. You can specify just a chromosome name, or a chromosome name and start postion, or a chromosome name and start and end position for the set of desired regions. 
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41 Minimum number of reads needed to consider a REF/ALT:
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43     This value declares the minimum number of reads containing a particular base at each position in order to list and use said allele in genotyping calls. Default is 0.
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45 Minimum base quality:
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47     The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
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49 Minimum mapping quality:
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51     The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
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53 Ploidy:
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55     The number of genotype calls to make at each reported position.
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57 Only write out positions with with possible alternate alleles:
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59     When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
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61 Report counts by strand:
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63     When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: <strand><BASE>=<COUNT>.
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65 Choose the dtype to use for storing coverage information:
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67     This controls the maximum depth value for each nucleotide/position/strand (when specified). Smaller values require the least amount of memory, but have smaller maximal limits.
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69         +--------+----------------------------+
70         | name   | maximum coverage value     |
71         +========+============================+
72         | uint8  | 255                        |
73         +--------+----------------------------+
74         | uint16 | 65,535                     |
75         +--------+----------------------------+
76         | uint32 | 4,294,967,295              |
77         +--------+----------------------------+
78         | uint64 | 18,446,744,073,709,551,615 |
79         +--------+----------------------------+
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84 **Citation**
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86 If you use this tool, please cite Blankenberg D, et al. *In preparation.*