voichek
commented
3 years ago Dear Jian,
With which of the problem do you want help?
- Regarding the error, did you try to run example 1 and did it work for you?
- LD - to calculate LD between k-mers and SNPs you just need the population presence/absence patterns of your associated k-mers and SNPs. For the k-mers - you can get those by using the
/bin/filter_kmersfunctionality. Then you can use any LD measure you want.
Best, Yoav
ytguojian
Hi Yoav,
We are performing the k-mer-based GWAS in peach using your kmersGWAS tools. We generated the bed file of k-mers, and used EMMAX to carry out GWAS. Because we got error in GWAS when running the kmers_gwas.py ,showing below.
"Traceback (most recent call last): File "/public/home/guojian/software/kmersGWAS-master/kmers_gwas.py", line 278, in
main()
File "/public/home/guojian/software/kmersGWAS-master/kmers_gwas.py", line 153, in main
fam_fn = get_file_type_in_dir(paths["kmers_associations_dir"], "%s.fam" % p_name)
File "/public/home/guojian/software/kmersGWAS-master/src/py/functions.py", line 10, in get_file_type_in_dir
raise Exception("File count not = 1 %s %d\n%s" % (type_suffix, len(fns), dir_name))
Exception: File count not = 1 phenotype_value.fam 0"
Therefore, we used EMMAX tool to perform GWAS. However, in the GWAS results, there were no position for the significant k-mers. So how to get the position, and how could we get the LD between SNP and K-mer. And how could we plot the fig in your NG article (such as,Fig. 1c, Fig. 4e,f)
we appreciate for that if you can help to solve the kmers_gwas.py error.
Thanks
Jian