blast_seed_to_indel.sh

#run in 05_ZhuWC directory
mkdir check_seed
cd check_seed
##blast seed to kinamaze genome
blat /home/lpeng/Gmatic5/genome/Rice_Kinamaze/Kinamaze_genome.fa seed_genes.fasta seed_gene_to_kinamaze.tsv
seqkit fx2tab -l seed_genes.fasta |cut -f 1,4

less -S seed_gene_to_kinamaze.tsv |cut -f 14,16,17,9,10|sed  '1,5d'|awk -v OFS="\t" '{print $3,$4,$5,$2,$1}'>OsRacGEF_gene_chr.bed

seqkit subseq --bed OsRacGEF_gene_chr.bed /media/galaxy/2efa4efe-25c8-4695-816e-e2df963b46e7/lpeng/Gmatic5/genome/Rice_Kinamaze/Kinamaze_genome.fa >OsRacGEF_gene_in_Kinamaze.fasta

seqkit subseq --bed OsRacGEF_gene_chr.bed /media/galaxy/2efa4efe-25c8-4695-816e-e2df963b46e7/lpeng/Gmatic5/genome/Rice_Kinamaze/Kinamaze_genome.fa >OsRacGEF_gene_in_kinamaze_up+down_3000.fasta

bedtools slop -i OsRacGEF_gene_chr.bed -g /home/lpeng/Gmatic5/genome/Rice_Kinamaze/Kinamaze_genome.size -l 3000 -r 3000 >OsRacGEF_gene_chr_3000.bed

less ../vcf/104-1-90-2_combined.flt.vcf|grep -v '#'|awk -v OFS="\t" '{print $1,$2-1,$2,$5}' >../vcf/104-1-90-2_combined.flt.bed

less ../vcf/104-3-1-90-2_combined.flt.vcf|grep -v '#'|awk -v OFS="\t" '{print $1,$2-1,$2,$5}' >../vcf/104-3-1-90-2_combined.flt.bed

bedtools intersect -a OsRacGEF_gene_chr_3000.bed -b ../vcf/104-1-90-2_combined.flt.bed -wa -wb -nonamecheck >104-1-90-2_combined.flt.indel_and_snp_in_OsRacGEF_gene.txt

bedtools intersect -a OsRacGEF_gene_chr_3000.bed -b ../vcf/104-3-1-90-2_combined.flt.bed -wa -wb -nonamecheck >104-3-1-90-2_combined.flt.indel_and_snp_in_OsRacGEF_gene.txt