FASTQ Simulation with known mutations

Question

[Raman2]

Hello!

Could anyone please suggest a tool which would simulate short reads with only mutations supplied by the user. I am trying to evaluate variant calling methods, and have a list of variants in specific gene locations and want to find out which methods would be best for finding the variants. So, basically I am looking for a tool which would take in reference fasta and vcf file and generate Fastq reads, but in addition to that I have 2 conditions - a) There should not any mutations apart from the intended location, b) the intended mutation should be in the intended location only in some of the reads and not all the reads (ie, if the read coverage in a particular region is 60x, the mutations should be only in say 20 or 30 reads and not in all the 60 reads)

I looked through some of the previous Biostar posts for read simulation, but couldn't exactly find the best tool.

Any suggestion would be greatly appreciated.

Thanks, Raman

Answer 1

[Pierre Lindenbaum]

convert a VCF to bam : vcf to bam

and then convert the bam to fastq using samtools fastq

[Raman2]

Thanks! But, Vcf to Bam will only create reads for the regions with mutations. I can't set the coverage for the rest of the reads

[Pierre Lindenbaum]

mix this ouput with the output of htslib/wgsim