obtain a simulated bam file for variants on existed bam file

Question

[J.F.Jiang]

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

Answer 1

[h.mon]

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

[J.F.Jiang]

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

Answer 2

[Pierre Lindenbaum]

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.

[J.F.Jiang]

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.

[bassanio]

Hi,

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

[h.mon]

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?