Comments (1)
Hi, Alexis-Catherine,
simuG introduces variants to the haploid version of the specified genome, with which you can further simulate reads on top of the variant-carrying genome output by simuG with any read simulators. So you can simulate two different haploid version of variant-carrying genomes by simuG, with some of variants shared between the two simulated haploid genomes (i.e., homozygous variants) and the other variants differ between the two simulated haploid genomes (i.e., heterozygous variants). Here is a potential protocol:
- Based on your ref_genome, simulate random variants with simuG to generate sim_genome1 and sim_vcf1.
- Take the output vcf file sim_vcf1 generated by simuG in step (1) for modification, during which you can control which variants to keep (which will be homozygous variants) and which variants to change (which will be heterozygous variants). Let's call this modified vcf file as sim_vcf2.
- Simulate specified variants with simuG using sim_vcf2 as the input to generate sim_genome_2.
- Now you will have sim_genome1 and sim_genome2, which share some homozygous variants relative to the ref_genome but also have some heterozygous variants that segregates between sim_genome1 and sim_genome2.
Hope this helps~
Best,
Jia-Xing
from simug.
Related Issues (14)
- bwa not generating sam file when provided with simulator's output HOT 3
- Use of uninitialized value in substr at simuG.pl line 1164. HOT 5
- how to simulate genomes with multiple types of variants HOT 2
- Argument "QUAL" isn't numeric in numeric ge (>=) at simuG.pl line 815, <$fh> line 6. HOT 3
- How to simulate SV (insertions and deletions) with length > 50bp? HOT 3
- Does simuG generate paired end data? HOT 2
- Use of uninitialized value in substr at [...] line 1158 HOT 3
- Changing power-law distribution alpha and constant HOT 2
- slow CNV creation HOT 3
- Issue with -gene_gff file.gff -coding_partition_for_snp_simulation "coding" HOT 13
- Uncertainty in description HOT 1
- Multicore execution HOT 1
- Uninitialize value when using gene gff option HOT 4
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from simug.