1. NorSim
Usage: norsim [options] <ref.fa> <nor.sim>
Options: -r FLOAT mutation rate of GV (0.0010000000)
-R FLOAT fraction of indels (0.000000)
-X FLOAT probability an indel is extended (0.300000)
-D FLOAT delete rate in indel (0.500000)
-B FLOAT BB rate in mutation (0.333330)
-I <delpos.txt> input long indel set file
-A <nor_AB.idx> output the positions of AB mutation type in normal
-o <nor_simout.txt> result for runing case
./norsim -r 0.001 -B 0 -A nor_AB.idx ref.fa nor.sim
2. TumSim
Usage: tumsim [options] <ref.fa> <base.sim> <nor_AB.idx> <subclone.sim>
Options: -r FLOAT mutation rate of SV (0.0000100000)
-R FLOAT fraction of indels (0.000000)
-X FLOAT probability an indel is extended (0.300000)
-D FLOAT delete rate in indel (0.500000)
-B FLOAT BB rate in mutation (0.333330)
-b FLOAT LOH BB rate in mutation (0.500000)
-A FLOAT mutation rate of LOH in normal AB (0.0000100000)
-p FLOAT the position of high desity (0.500000)
-n int mutation number in high desity (100)
-l int length of high desity (100000)
-I <indelpos.txt> input long indel set file. generating <subclone.sim.idx> for 'ReadGen'
-N <other_chged.idx> input changed positions in other subclone(may multi-choices)
-C <*_chged.idx> output changed positions in this turmor
-o <*_simout.txt> output result for runing case
./tumsim -r 0.007 -A 0 -B 0 -n 7000 -p 0 -l 100000 ref.fa nor.sim nor_AB.idx s1.sim
./tumsim -r 0.003 -A 0 -B 0 -n 3000 -p 0 -l 100000 ref.fa s1.sim nor_AB.idx s2.sim
3. ReadGen
Usage: readgen [options] <ref.fa> <*.sim> <left.fq> <right.fq>
Options: -d INT outer distance between the two ends of paired_end reads [10000]
-s INT standard deviation of MAX_DIS [10]
-l INT length of left read [100]
-r INT length of right read [100]
-c float cover rate of read [5.000000]
-e float error r ate in generate reads [0.000000]
-S output single read(not paired_end reads)
-k keep 'N' character in reads
-I <subclonde.sim.idx> long insert table file from 'TumSim'
-O <genread.log> result for runing case
./readgen -l 250 -r 250 -d 1000 -s 10 -c 30 ref.fa nor.sim n30_left.fq n30_right.fq
./readgen -l 250 -r 250 -d 1000 -s 10 -c 50 ref.fa s1.sim s1_left.fq s1_right.fq
./readgen -l 250 -r 250 -d 1000 -s 10 -c 20 ref.fa s2.sim s2_left.fq s2_right.fq
4. Merge
Usage: merge ref_name *1.fq ... *n.fq all.fq
./merge chr16 n30_left.fq s1_left.fq s2_left.fq t100_left.fq
./merge chr16 n30_right.fq s1_right.fq s2_right.fq t100_right.fq
5. BWA
bwa index -a bwtsw ref.fa
bwa aln ref.fa t100_left.fq>t100_left.sai
bwa aln ref.fa t100_right.fq>t100_right.sai
bwa sampe -f p1.sam ref.fa t100_left.sai t100_right.sai t100_left.fq t100_right.fq
6. VPE
Usage: vpe readlength ref.fa vpoint.sim in.sam out.vaf VPEname
./vpe 250 ref.fa s2.sim p1.sam 1.vaf VPE1
7. Misspoint
Usage: misspoint vpoint.sim VPEname1 insertsize1 VPEname2 insertsize2 outname
./misspoint s2.sim VPE1 1000 VPE2 1500 missp
8. VPEapart.py
Usage: input: VPE
output: apart file
9. mapAB.py
Usage: input: .xlsx (process apart file to excel file) and ref.xlsx (turn ref.fa to excel file)
output: VPE_variants_AB (merge them to VPEAB.txt)
10. SciClone
[https://github.com/genome/sciclone]
11. Sci-cluster
Usage: sc cluster.txt cluster
./sc cluster.txt siclus
12. Haplotype
Usage: haplotype vpoint.sim cluster VPEname1 insertsize1 VPEname2 insertsize2 VPEname2 insertsize3 out
./haplotype s2.sim siclus VPE1AB.txt 1000 VPE2AB.txt 1500 VPE3AB.txt 2000 short_chain
13. weight_matrix.py
Usage: input:
positionAB.xlsx (apart short_chain into positionAB and variantsAB)
variantsAB.xlsx (apart short_chain into positionAB and variantsAB)
cluster.xlsx (turn siclus into excel file)
output:
w.mat (weighted matrix)
w0.mat (weighted matrix for the founding clone variants)
ww.mat (weighted matrix after thickness stripping)
14. none_zero.m
Usage: input: w0.mat and ww.mat
output: w0_nonezero.mat and a0.mat
ww_nonezero.mat and aww.mat
15. max_spanning_tree.py
Usage: input:
ww_nonezero.mat
aww.mat
output: chainAB.txt
16. Re-cluster
Usage: rc vpoint1.sim vpoint2.sim vpoint3.sim realcluster realchain
17. rechainmapped.py
Usage: input: rchain.xlsx
output: rechainAB.txt
18. Check
Usage:check realcluster realchain chain
./ck reclus rechainAB.txt chainAB.txt