Is there a tool that can scan fastq files without assembling them for a custom list of user defined snps?
Try this pipeline:
- Clean raw fastq files (trimmomatic)
- Align clean fastq files to the reference genome (dna-to-dna aligner of your choice)
- Convert the alignment sam file to bam (samtools)
- Call SNPs from bam file (samtools)
Here's a start tutorial on this: http://ged.msu.edu/angus/tutorials-2013/snp_tutorial.html
You could use ARIBA, which will map you reads to the regions of your interest (more on that in a second) and then assemble/call variants.
The tool is mostly used to find known variants related to AMR (antimicrobial resistance) from a set of databases, but according to the project's wiki you can build your own database with your region of interest.
Additionally, reference sequences can be either of: Presence/absence sequences. ARIBA will look for these sequences in the input reads and report any that it finds, and also any variants between these sequences and the input reads. Variants only sequences. These should have known variant details specified in the metadata file (see below). ARIBA reports only when it finds at least one of the given variants in each of these these sequences. If a sample has one of these sequences, but does not have one of the supplied variants, then it is not reported. If you supply a variants only sequence, but no variant, then the sequence will be removed during sanity checks.