# HG changeset patch # User Daniel Blankenberg # Date 1377629689 14400 # Node ID 69d5400f3186d4480ca27556ee853f83390f706c # Parent 66a4325d939437abcf3ac5a07d4f9f488f41a582 update readme diff -r 66a4325d9394 -r 69d5400f3186 README.rst --- a/README.rst Tue Aug 27 14:37:12 2013 -0400 +++ b/README.rst Tue Aug 27 14:54:49 2013 -0400 @@ -23,60 +23,60 @@ 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,`` + ``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,`` + ``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. + 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. + 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. + 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. + 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. + 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. + 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. + 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: =. + When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: =. 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. + 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 | - +--------+----------------------------+ + +--------+----------------------------+ + | name | maximum coverage value | + +========+============================+ + | uint8 | 255 | + +--------+----------------------------+ + | uint16 | 65,535 | + +--------+----------------------------+ + | uint32 | 4,294,967,295 | + +--------+----------------------------+ + | uint64 | 18,446,744,073,709,551,615 | + +--------+----------------------------+ ------ diff -r 66a4325d9394 -r 69d5400f3186 tools/naive_variant_detector.xml --- a/tools/naive_variant_detector.xml Tue Aug 27 14:37:12 2013 -0400 +++ b/tools/naive_variant_detector.xml Tue Aug 27 14:54:49 2013 -0400 @@ -126,60 +126,60 @@ 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,`` + ``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,`` + ``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. + 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. + 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. + 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. + 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. + 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. + 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. + 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>. + 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. + 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 | - +--------+----------------------------+ + +--------+----------------------------+ + | name | maximum coverage value | + +========+============================+ + | uint8 | 255 | + +--------+----------------------------+ + | uint16 | 65,535 | + +--------+----------------------------+ + | uint32 | 4,294,967,295 | + +--------+----------------------------+ + | uint64 | 18,446,744,073,709,551,615 | + +--------+----------------------------+ ------