Question: obtain a simulated bam file for variants on existed bam file
1
gravatar for J.F.Jiang
4.8 years ago by
J.F.Jiang820
China
J.F.Jiang820 wrote:

Hi all,

I constructed the variant calling pipeline for BAM file. However, when it was applied to positive samples, I did not find any well-known variants in the VCF file. What I am considering is that there might be less-sensitive method in my pipeline.

So I want to create a simulated BAM file based on the existed bam, just change the reads in the bam to create a variant, etc., rs6071.

Is there any convenient tool to do such, and also can I obtain a depth-aimed bam? For example, depth for alleles, A:G, 500:500, OR A:G, 800:200.

 

Thanks

variant bam simulated • 2.0k views
ADD COMMENTlink modified 4.8 years ago by h.mon30k • written 4.8 years ago by J.F.Jiang820
1
gravatar for h.mon
4.8 years ago by
h.mon30k
Brazil
h.mon30k wrote:

BAMSurgeon seems to be able to do what you want (and much more).

ADD COMMENTlink written 4.8 years ago by h.mon30k

Exactly what I am looking for though bugs are still in this program needing debug

ADD REPLYlink written 4.7 years ago by J.F.Jiang820
0
gravatar for Pierre Lindenbaum
4.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

extract the region of interest as fasta, add manually the mutation, run wgsim to create a set of fastq and map those fastqs using your pipeline.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Pierre Lindenbaum129k

Thanks, wgsim can works fine to simulate a set of fastq with mutations, however, the program will randomly select mutation site in the given intervals. What I want to is to mutate the specific site, and can change the alleles depth seperately.

ADD REPLYlink written 4.8 years ago by J.F.Jiang820

Hi,

Where you able to perform this task. if so can you please let us know

ADD REPLYlink written 8 months ago by bassanio20

Are you aware you are resurrecting a four-years old thread?

Did you read the manual and tried to use BAMSurgeon? In this case, did you run into any problems in running BAMSurgeon?

ADD REPLYlink written 8 months ago by h.mon30k
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