| Next changeset 1:ae6edc0012ba (2013-08-29) |
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Commit message:
Create naive_variant_caller repository |
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README.rst |
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| diff -r 000000000000 -r 0fa83c466e9d README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Aug 29 09:57:14 2013 -0400 |
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| @@ -0,0 +1,86 @@ +This repository contains the **Naive Variant Caller** tool. + +------ + +**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.* |