# HG changeset patch
# User Daniel Blankenberg <dan@bx.psu.edu>
# Date 1377626202 14400
# Node ID 162baa0e4db4b81cf4064099ece76475affab476
# Parent  7f654ba273cb2f5f4cd304e0991a77800dfa572a
update readme

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diff -r 7f654ba273cb -r 162baa0e4db4 README.rst
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+This repository contains the Naive Variant Caller.
+
+------
+
+**What it does**
+
+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. 
+
+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. 
+
+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.
+ 
+
+------
+
+**Inputs**
+
+Accepts one or more BAM input files and a reference genome from the built-in list or from a FASTA file in your history.
+
+
+**Outputs**
+
+The output is in VCF format.
+
+Example VCF output line, without reporting by strand:
+ ``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,``
+
+Example VCF output line, when reporting by strand:
+ ``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,``
+
+**Options**
+
+Reference Genome:
+
+  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.
+
+Restrict to regions:
+
+ 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. 
+
+Minimum number of reads needed to consider a REF/ALT:
+
+ 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.
+
+Minimum base quality:
+
+ The minimum base quality score needed for the position in a read to be used for nucleotide counts and genotyping. Default is no filter.
+
+Minimum mapping quality:
+
+ The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
+
+Ploidy:
+
+ The number of genotype calls to make at each reported position.
+
+Only write out positions with with possible alternate alleles:
+
+ When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
+
+Report counts by strand:
+
+ When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: <strand><BASE>=<COUNT>.
+
+Choose the dtype to use for storing coverage information:
+
+ 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.
+
+ +--------+----------------------------+
+ | name   | maximum coverage value     |
+ +========+============================+
+ | uint8  | 255                        |
+ +--------+----------------------------+
+ | uint16 | 65,535                     |
+ +--------+----------------------------+
+ | uint32 | 4,294,967,295              |
+ +--------+----------------------------+
+ | uint64 | 18,446,744,073,709,551,615 |
+ +--------+----------------------------+
+
+------
+
+**Citation**
+
+If you use this tool, please cite Blankenberg D, et al. *In preparation.*