Entering edit mode
12 days ago
noodle
▴
580
Hi all,
Looking for resources for free software/packages that accept fastq files (or bam) as input and return a '23 and me-like' output. Either health- or ancestry-oriented, the only criteria are free, comprehensive/accurate, and navigable outputs (eg html)!
I was hoping something like multiqc exists for this, but have yet to find something, surprisingly...
TIA!
Noted that 'accurate' wasn't among your criteria ;)
Anyway, most variant callers are free open-source software. However, for ancestry analysis you need a reference panel. I think 23 use their customer data with consent (not sure if they can use other sources like 1000 genomes). For health-related phenotypes, you need to integrate GWAS results with alleles. My best bet is to use dbSNP with together OMIM.
If you google the title of this post, you will find the usual offers of 'free' analysis, but beware, there is no free lunch. Initial payment is that they have your data and can use it as they like.
I haven't tried them and don't want to endorse or recommend any here but you will certainly find them.
Thank you, I added 'accurate' now ;)
I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this information into a concise, user-friendly report. It's been a decade(s?) since all these tools and data were publicly available.
Accurately assessing a few QC metrics is trivially easy.
Assessing the significance of variants in a clinically responsible way is really, really hard.