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Readme.txt 2014-07-10 1.4 kB
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SVHapSimulator_v0.1 2014-07-10 53.2 kB
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simulate_high_coverage.sh 2014-07-10 1.1 kB
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Totals: 3 Items   55.6 kB 0 
1. Usage: ./SVHapGnrtor [options] 

                  -D/I      For deletions/insertions
                  -h        help

Options for Deletion;
                  -v FILE   Deletion postion and genotype file
                  -i INT    Total number of individuals
                  -c FILE   Chromosome file
                  -s INT    Number of simulated individuals

Options for Insertion;
                  -v FILE   Insertion position and length file
                  -i INT    Number of individuals to simulate
                  -c FILE   Chromosome file
                  -z INT    % of 0/0
                  -o INT    % of 0/1
                  -t INT    % of 1/1, 0/0 add 0/1 and 1/1 should be 100.


2. Simulate haplotypes with deletions
Example:
./SVHapSimulator -D -v 15.hg19.genotype.txt -c /reference/chr15.fa -s 2 -i 45

Format of "-v File":
chrom delete_id leftmost_position rightmost_position genotype_info
Example Format of "-v File"
15 P1_M_061510_15_385 18847456 18847615 0/1:99:-1000.00,0.00,-1000.00:PASS 0/0:3:-0.16,-0.51,-1000.00:LowQual 0/0:17:-0.01,-1.73,-1000.00:PASS

3. Simulate haplotypes with insertions
Example:
./SVHapSimulator -I -v /Insertion/chr11.insertion.bed -c /Reference/hg19/chr11.fa -i 2 -z 33 -o 33 -t 34

Format of "-v File":
chrom position insertion_length
Example of "-v File":
11 418014 292
Source: Readme.txt, updated 2014-07-10