Simulate Ngs Reads With Exact Mutations (Snp, Indel Etc.) , Frequency , Forward / Rev Ratio Etc. Parameters

Question

[saurindjani]

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

[Istvan Albert]

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.

Answer 1

[chen]

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
        }
    ]
}

[Istvan Albert]

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.

[chen]

Thanks, good advices!