Hi, I just wrote a SeqMaker which can simulate Next Generation Sequencing data with mutations
https://github.com/OpenGene/SeqMaker.jl
The mutation is configured in a JSON config file.
{
"config":{
"depth":300,
"pair-end":true,
"readlen":151,
"assembly":"hg19",
"seq_error_rate":0.001,
"template_len":{
"min":140,
"max":200
},
"normal_base_qual":{
"min":30,
"max":37
},
"seq_error_qual":{
"min":8,
"max":20
}
},
"fusion":[
{
"name":"ALK-intron19-EML4-intron13",
"left":"-2:29447873",
"right":"+2:42526793",
"rate":0.1
}
],
"snv":[
{
"name":"EGFR-L861Q",
"chrom":"chr7",
"pos":55259524,
"ref":"T",
"alt":"A",
"rate":0.2
},
{
"name":"KRAS-G12D",
"chrom":"chr12",
"pos":25398284,
"ref":"G",
"alt":"A",
"rate":0.75
}
]
}
this is not a common need, usually the read simulators will generate a mutated genome with some characteristics. In your case I am afraid you would need to actually create a custom genome then run a simulator where you turn off the mutation rates.