Hi,
I am recently using Sim-it (v1.4.4) to simulate specific structural variants (SVs) based on a provided VCF file.My goal is to simulate a genome containing the exact sequences defined in my input VCF.
(simit_env) [zhaoshuo@ln01 input_vcf]$ head C001.vcf.bak
01 2108 207 INS 1/0 TTTCCAGGGCACCGGACATCCGAGGCCCGAGTTATGGCCGTTTGAATTTACTTTTTCCTTTCTCATCATATTTCTACTCGCCTAAGAATGAGCAAAAGGCATTTTTCGAAGAATCGGTTTGCTCAAACCGCCTTACGTCGGTACGGTTGCGTAGATATCGAAAAAATACGCAGGTTCACAAAAAAAATCGACTGAAAACGCCTTACGG
01 3961 186 INS 1/0 GTTTTCTGAAAAATCAGATCGCTCAAACCCCGTCGCGACGTTTCGGTTGAGTAGATATCGTAAAGATATGCAGGTTCAAAAAAAAAAATTCCTGAAACGGACGTCCGAAACTCGAGTTATGACCGTTTGAATTTCCTTTTTGCTTTCTCATCTTATTTCTACTCGCCTAAGAATGATCAAAAGGCGT
01 12901 182 INS 1/0 AATATGCAGGTTAAAAAAAAACGGTAGAAACGGACGTCCGAAGATCGAGTTATGGCCGTTTGAATTTCCTTTTTCCTTTCTCATCTTATTTCTACTCGCCTAAAAATGAGCAGAAGGCGTTTTCTGAAAAATCAGATCGCTCAAACCCCGTCGCGACGTTTCGGTTGAGTAGATATCGTAAAG
......
However, in the output VCF generated by Sim-it, both the REF and ALT columns contain only a single, identical nucleotide. Furthermore, the specified sequences from my input were not found in the simulated genome. I also tried providing the sequences in a separate FASTA file and referencing them in the VCF, but I got the same incorrect result.
Attached below are my config file and the resulting output VCF.
Project:
-----------------------------
Project name = real_01
Reference sequence = /public/home/zhaoshuo/work1/data/reference/DM8.1_genome.ori.chr.fa
Replace ambiguous nts(N) = Yes
Max threads = 8
Seed = 121
Structural variation:
-----------------------------
VCF input = /public/home/zhaoshuo/work1/simulation/input_vcf/C001.vcf
Foreign sequences = /public/home/zhaoshuo/work1/simulation/input_vcf/C001.fa
Deletions = 0
Length (bp) = 50-100000
Insertions = 0
Length (bp) = 50-100000
Tandem duplications = 0
Length (bp) = 50-10000
Copies = 1-10
Inversions = 0
Length (bp) = 50-1000000
Complex substitutions = 0
Length (bp) = 30-1000
Inverted duplications = 0
Length (bp) = 150-10000
Heterozygosity = 0%
Long Read simulation:
-----------------------------
Sequencing depth = 0
Median length = 15000
Length range = 500-100000
Accuracy = 90%
Error profile = error_profile_ONT.txt
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
01 2108 1 T T . PASS SVTYPE=INS;SVLEN=207 GT 1/0
01 3961 2 G G . PASS SVTYPE=INS;SVLEN=186 GT 1/0
01 12901 3 A A . PASS SVTYPE=INS;SVLEN=182 GT 1/0
01 14709 4 TAAAAATATGCAGGTTCAAAAAAAATCTGAACGGACATCAAACCGAGTTATGGCGTTTGAATTTCCTTTTGCTTTAAGATCTTTATTTCTACTCGTATAAGAATGATCAAAAGGCGTTTTCTTAAAATCGGATCGCTCAAA T . PASS SVTYPE=DEL;SVLEN=71 GT 1/0
01 17146 5 T T . PASS SVTYPE=INS;SVLEN=323 GT 1/0
01 18410 6 TTTTCGTTATATTTCTACTCGTATAAGAATGGGCAAAAGGCGTTTTTCGAAAAATCGGATCGCTCAAACCCGTCGCGACGTTTGGGTTGAGTAGATATAGTAAAAATATGCAGGTCCAAAAAAAAATTCGCCTGAAACGGACGTCCGAAGCTCGAGTTATGGCCGTTTGAATTTCCTTTTTCC T . PASS SVTYPE=DEL;SVLEN=172>
01 25091 7 T T . PASS SVTYPE=INS;SVLEN=187 GT 1/0
01 29910 8 TATTTTTTCGAGATCTATTCGAAAAAGTCATTCGCATTCGTTGAATTTCATTTTAATTTTTTCGTTATATTCCAACTCGTATGAGAATGAGCGAAGAGGCGTTTTCTGAAAAATCGGATCGCTCAAACCGCGTCGCGACGTTTCGGTTGAATAGATATCGTAAAAATATGCAGGTTCAAAAAAATAATCGCCTCAAACGGACGTCCGAAGCCCGAGTTATGGCCGTTT>
01 31690 9 AAAATCGGCTCGCTCAAACCGCCTTCTGGCGGTTCGGTTCGTGAATATCGAAAAAATACGCAGGTTCAAAAAAAAATCGACTAAACGGACATCGAGGCCCGAGTTATGGCCGTTTGAATTTCTTTTCCGGCACCTTGCCTTTAAGATCTTTGAATTTTGAATGATCGTAACTTCGACTCGAGCGTCCTTTTAGCGCAATTTTTTTGATCCCTCGTATTTTTTCGAGAT>
01 33860 10 CACCGTCGGCCTTTAAGATGCTGAATTTTCGAATGATCGTACCTTTCGACTCGAACGACCTTTTGACGCAATTTTTTTTTTGATCCCTCGTATTTTTTCGAGATCTATTCGAAAAACACATTCGCATTCGCTGAATTTCATTTTAATTTTTCGTTATATTTCTACTCGTATAAGAATGGGCAAAAGGCGTTTTTCGAAAATCGGATCGCTCAAACCCGTCGCGACGTT>
01 35727 11 T T . PASS SVTYPE=INS;SVLEN=156 GT 1/0
01 37104 12 GGCCGTTTGAATTTACTTTTCCTTTCTCATCTTATTTCTACTACGCCTAAGAATGAGCAAAAGGCGTTTTTCGAAAAATCGGCTCGCTCAAACCGCCTTCTGGCGGTTCGGTTCGTGAATATCGAAAATACGCAGGTTCAAAAAAAATCGTTGAAACGGACATCGAGGCCCGAGTTATGGCCGTCTGAATTAACTTTTTTCCCGGGCACCTTCGACCTTTAAGATGCT>
01 41823 13 C C . PASS SVTYPE=INS;SVLEN=316 GT 1/0
01 49277 14 CCTGAATTTCATTTTAATTTTTTCGTTATATTTCTACTCGTATAAGAATGGGCAAAAAGGCGTTTTCTGAAAAATCGGATCGCTCAGACCCTGTCGCGACGTGTCGGTTGAGTAGATATCGTAAAAATATGCAGGTTCAAAAAAAAAATCGCCTAAAACGGACGTCCGAAGCTCGAGTTATGGCCGTTTGAATTTCCTTTTTCCTTTCTCATCTTATTTCTACTCGCC>
01 49277 15 G G . PASS SVTYPE=INS;SVLEN=185 GT 1/0
Thank you for your help.
Hi,
I am recently using Sim-it (v1.4.4) to simulate specific structural variants (SVs) based on a provided VCF file.My goal is to simulate a genome containing the exact sequences defined in my input VCF.
(simit_env) [zhaoshuo@ln01 input_vcf]$ head C001.vcf.bak
However, in the output VCF generated by Sim-it, both the REF and ALT columns contain only a single, identical nucleotide. Furthermore, the specified sequences from my input were not found in the simulated genome. I also tried providing the sequences in a separate FASTA file and referencing them in the VCF, but I got the same incorrect result.
Attached below are my config file and the resulting output VCF.
Thank you for your help.