Question: Simulate Ngs Reads With Exact Mutations (Snp, Indel Etc.) , Frequency , Forward / Rev Ratio Etc. Parameters
1
gravatar for saurindjani
6.0 years ago by
saurindjani10
saurindjani10 wrote:

Hi there,

I have list of exact mutations (snp, indel etc.) and frequencies. Could you please help me (point me to correct software or program if any one has encountered this type of problem) so, I can create a simulated NGS reads and run variant caller on those snp and indels?

thanks, Saurin

reads ngs • 2.1k views
ADD COMMENTlink modified 3.7 years ago by chen1.9k • written 6.0 years ago by saurindjani10

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.

ADD REPLYlink written 6.0 years ago by Istvan Albert ♦♦ 81k
2
gravatar for chen
3.7 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

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
        }
    ]
}
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by chen1.9k
1

I would recommend posting it as a separate announcement and not as an answer to a two year old post. Also your README needs to provide a minimal information on how to run the tool. Looking at the example code I had no idea what language is it even written in. Turns out it is Julia right?

Make your tool easy to use and you'll see that its adoption will rise accordingly.

ADD REPLYlink written 3.7 years ago by Istvan Albert ♦♦ 81k

Thanks, good advices!

ADD REPLYlink written 3.7 years ago by chen1.9k
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