<p>I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of vcf. How to do that?</p>
<p>The GIAB project has gold standard vcf, bam, and fastq. But they are not perfect for pipeline testing. Their size is quite big. Also, they are real data. My question was how to generate simulated Bam from vcf.</p>

CC BY-SA 4.0
2023-11-28T14:51:54.270Z
Have you tried making a modified fasta containing the variants and then simulated reads using that. Normally then you'd mix those together with reads simulated against the reference sequence at different ratios.
Devon Ryan
CC BY-SA 4.0
2023-11-28T15:20:27.490Z
Actually, I am planning to do that now. The thing is, I couldn't determine which one is the most convenient way. I am planning to do that using Python. Can you write it in the answer and suggest a convenient way to do that?
Shafayet Rahat
CC BY-SA 4.0
2023-11-28T21:47:33.397Z
Hint, you want to make a fasta from a VCF (e.g., https://www.biostars.org/p/360900/) and then use any random read simulator. No need to program anything, that'd be a waste of time.
Devon Ryan
CC BY-SA 4.0
2023-11-29T18:23:16.630Z
Sorry, I didn't read your comment earlier properly. Actually, I used many simulators like NEAT, ART, MASON, etc. But, unfortunately, they are too much buggy. If you go to their issues, you will see their problems. That's why I wanted to write my own code in the first place. However, among the simulators, NEAT probably is the least buggy one.
Shafayet Rahat
<sam><vcf><format-conversion><simulated-data><conversion>
Generate simulated bam for certain snps
# Generate simulated bam for certain snps

(Asked by: username_0 on 2023-11-23)

I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of vcf. How to do that?

The GIAB project has gold standard vcf, bam, and fastq. But they are not perfect for pipeline testing. Their size is quite big. Also, they are real data. My question was how to generate simulated Bam from vcf.

**Tags:** sam, vcf, format-conversion, simulated-data, conversion
> **Comments:**
> **username_1**: Have you tried making a modified fasta containing the variants and then simulated reads using that. Normally then you'd mix those together with reads simulated against the reference sequence at different ratios.  
> **username_0**: Actually, I am planning to do that now. The thing is, I couldn't determine which one is the most convenient way. I am planning to do that using Python. Can you write it in the answer and suggest a convenient way to do that?  
> **username_1**: Hint, you want to make a fasta from a VCF (e.g., https://www.biostars.org/p/360900/) and then use any random read simulator. No need to program anything, that'd be a waste of time.  
> **username_0**: Sorry, I didn't read your comment earlier properly. Actually, I used many simulators like NEAT, ART, MASON, etc. But, unfortunately, they are too much buggy. If you go to their issues, you will see their problems. That's why I wanted to write my own code in the first place. However, among the simulators, NEAT probably is the least buggy one.  

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## 0 answers

