Homework 2

BEDTools

Recently the 3000 Rice genome project released data on resequencing 3000 rice genomes. See the site here and OryzaSNP.

You can access this file in the SNPs link below

I downloaded the Rice GFF annotation from Gramene from this FTP location

Use the following files SNPs and annotation

1. How many genes have SNPs that overlap them?
2. How many SNPs are in the coding regions of genes (denoted by the CDS feature)?

(note you don't need to DO any of the following to do the homework, I am providing you information on how the files were obtained)

For your reference. I downloaded SNP data with allele frequency info from the Rice 3K project (no need for you to download the whole file). I then converted it to BED format and retained only the Chr6 data.

    wget http://oryzasnp-atcg-irri-org.s3-website-ap-southeast-1.amazonaws.com/3krg-3k_filt_snp-v1/3k_filtered.map.gz
    wget http://oryzasnp-atcg-irri-org.s3-website-ap-southeast-1.amazonaws.com/3krg-3k_filt_snp-v1/3k_filtered.ped.gz
    gunzip *.gz
    plink --file 3k_filtered --recode vcf-iid -out 3k_filtered.SNP_filt
    grep ^6 3k_filtered.SNP_filt.vcf  > chr6_3kSNP_filt.vcf
    awk 'BEGIN{OFS="\t"} {print $1,$2-1,$2}' chr6_3kSNP_filt.vcf > rice_chr6_3kSNPs_filt.bed