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update readme
author Daniel Blankenberg <dan@bx.psu.edu>
date Tue, 27 Aug 2013 14:54:49 -0400
parents 66a4325d9394
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21 **Outputs** 21 **Outputs**
22 22
23 The output is in VCF format. 23 The output is in VCF format.
24 24
25 Example VCF output line, without reporting by strand: 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,`` 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,``
27 27
28 Example VCF output line, when reporting by strand: 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,`` 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,``
30 30
31 **Options** 31 **Options**
32 32
33 Reference Genome: 33 Reference Genome:
34 34
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. 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.
36 36
37 Restrict to regions: 37 Restrict to regions:
38 38
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. 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.
40 40
41 Minimum number of reads needed to consider a REF/ALT: 41 Minimum number of reads needed to consider a REF/ALT:
42 42
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. 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.
44 44
45 Minimum base quality: 45 Minimum base quality:
46 46
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. 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.
48 48
49 Minimum mapping quality: 49 Minimum mapping quality:
50 50
51 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter. 51 The minimum mapping quality score needed to consider a read for nucleotide counts and genotyping. Default is no filter.
52 52
53 Ploidy: 53 Ploidy:
54 54
55 The number of genotype calls to make at each reported position. 55 The number of genotype calls to make at each reported position.
56 56
57 Only write out positions with with possible alternate alleles: 57 Only write out positions with with possible alternate alleles:
58 58
59 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output. 59 When set, only positions which have at least one non-reference nucleotide which passes declare filters will be present in the output.
60 60
61 Report counts by strand: 61 Report counts by strand:
62 62
63 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: <strand><BASE>=<COUNT>. 63 When set, nucleotide counts (NC) will be reported in reference to the aligned read's source strand. Reported as: <strand><BASE>=<COUNT>.
64 64
65 Choose the dtype to use for storing coverage information: 65 Choose the dtype to use for storing coverage information:
66 66
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. 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.
68 68
69 +--------+----------------------------+ 69 +--------+----------------------------+
70 | name | maximum coverage value | 70 | name | maximum coverage value |
71 +========+============================+ 71 +========+============================+
72 | uint8 | 255 | 72 | uint8 | 255 |
73 +--------+----------------------------+ 73 +--------+----------------------------+
74 | uint16 | 65,535 | 74 | uint16 | 65,535 |
75 +--------+----------------------------+ 75 +--------+----------------------------+
76 | uint32 | 4,294,967,295 | 76 | uint32 | 4,294,967,295 |
77 +--------+----------------------------+ 77 +--------+----------------------------+
78 | uint64 | 18,446,744,073,709,551,615 | 78 | uint64 | 18,446,744,073,709,551,615 |
79 +--------+----------------------------+ 79 +--------+----------------------------+
80 80
81 81
82 ------ 82 ------
83 83
84 **Citation** 84 **Citation**