Question: Samtools Wgsim: Creating A Mutation At A Given Position.
0
gravatar for Pierre Lindenbaum
8.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum130k wrote:

I'll be giving a course about NGS and I'd like the students hunting for some well defined non-synonymous variations in the domain of a given protein .

My 1st idea : duplicating one chromosome , inserting a mutation and let samtools wgsim generating the (heterozygous) mutations.

2nd idea: changing the source code of wgsim . However it's not clear to me where I should put my snippet of C code to insert the mutation; Do you have any idea ? Thanks.

samtools simulation C code • 3.8k views
ADD COMMENTlink written 8.8 years ago by Pierre Lindenbaum130k

seems simplest to either modify the reference or get the reads from some publication that found such a variant.

ADD REPLYlink written 8.8 years ago by brentp23k
3
gravatar for lh3
8.8 years ago by
lh332k
United States
lh332k wrote:

If you prefer to modify the source code, see the "wgsim_print_mutref()" function. It takes two haploid sequences "hap1" and "hap2" (more exactly, haploid differences from the reference) as input and prints out all the differences from the reference. The lower two bits keep the actual sequence. Once you understand how that works, it is easy to generate these sequences.

BTW, an updated version is here, with some bug fixes.

ADD COMMENTlink written 8.8 years ago by lh332k
0
gravatar for lyz10302012
8.0 years ago by
lyz10302012360
China
lyz10302012360 wrote:

Hi Pierre,

I also want to do same job as your 1st idea. The step is, 1) Create two sequences of the diploid. 2) Simulate het and homo variants in these two sequences. 3) Simalate sequencing reads

Did you solve this problem? or do you konw how to solve it?

Thanks.

ADD COMMENTlink written 8.0 years ago by lyz10302012360
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