Hi, I have coordinates in bed format and i am interested to associate SNP with the segments. I looked at plink format but here data is in tsv format. I tried to convert tsv format to bed format but there are multi-SNP haplotypes or SNP-SNP interactions. (Here is sample file link) "GWAS Sample File.tsv"
The sample file was prepared from GWAS catalog. https://www.ebi.ac.uk/gwas/
The column no 12 "CHR_ID" and 13 "CHR_POS" contains different SNP positions for same phenotype. I want to split this info for each SNP on each line. Is there any possible way?
How can i process GWAS data? Is there any tool available to search multiple SNPS on bash?
Thanks in advance.
Regards
Muhammad Shahbaz Munir
Mphil Scholar
0 answers
No answers yet.
Log in to answer this question.
-
Significant SNPs with the same effect in FarmCPU
written by Noctiluca •
-
KING relatedness inference hanging
written by marcus.tutert •
-
Preparing Target Data
written by Jenish •
-
EpiMap enhancer data access
written by michael.j.apostolides •
-
Problem with CNVkit using samples with single-end sequenced WES
written by tangya1982 •
-
Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
written by michael.nagle
-
Process GWAS data?
written by shahbazmunir11 •
-
vcftools returns no vcf output after filtering
written by wes3985 •
-
SHAPEIT allele encoding
written by andreagarcia871
-
How to create B-allele frequency file for ADTEx?
written by Dataman
