QTL mapping by GBS
Entering edit mode
3.5 years ago
soniabedi.07 ▴ 30

Can anyone help me in understanding the workflow for QTL mapping by GBS. How is filtering of SNPs done?? what parameters need to be set.


SNP • 805 views
Entering edit mode
6 months ago
rimgubaev ▴ 300

To perform QTL mapping of the using GBS/RAD-seq one first need to perform a SNP calling using pipelines which could specifically developed for GBS/RAD-seq like TASSEL-GBS or WGS SNP calling pipelines like GATK that were adapted for GBS/RAD-seq, here you can find an example of such pipeline. Next you proceed with the SNP filtering and here a kind of art starts. I would recommend to filter for average genotype sequencing depth, proportion of genotyped individuals and MAF. Additionaly one should select SNPs that were genotyped in both parents, this step is crucial for genetic map construction. If you coverage is low it is possible to impute missing genotypes using tools like LB-impute pipeline specifically developed for mapping populations. Next one need to prepare a vcf filtered and imputed file for genetic map construction and QTL-mapping tools like r/qtl. Note for genetic map construction you need additionally filter your genotypes according to the expected segregation ratio i.e 1:2:1 for F2 cross and 1:1 for backcross (BC). Here is an example paper of QTL mapping based in GBS data. Good luck!


Login before adding your answer.

Traffic: 1045 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6