Hi Guys,
I have a question regarding the annotation of SNPs. I have list of candidate SNPs with chr ids (file 1) and the their positions and another file (file 2) I have a gft file with chr id, gene positions (start and stop) and genes names. I am looking to fetch the positions of SNPs (file 1) in between the positions of genes (file 2). I tried bedtools however I could not file the command. Please advise any options to deal with this analysis.
File 1:
chr1 271353586 T
chr1 897272822 C
chr1 913363908 T
File 2:
chr1 271353222 371353586 Gene1
chr1 897272522 897272822 Gene2
chr1 583821554 583821710 Gene3
1 answer
The problem you may have is that the SNP file contains only positions, and bedtools expects regions. If you convert your position file into a bedfile then you could use bedtools intersect to achieve the desired results:
$ cat file1.txt
chr1 271353586 T
chr1 897272822 C
chr1 913363908 T
$ cat file2.bed
chr1 271353222 371353586 Gene1
chr1 897272522 897272822 Gene2
chr1 583821554 583821710 Gene3
$ awk 'OFS="\t"{print $1, $2-1, $2, $3}' file1.txt \
| bedtools intersect -a file2.bed -b - -wao
chr1 271353222 371353586 Gene1 chr1 271353585 271353586 T 1
chr1 897272522 897272822 Gene2 chr1 897272821 897272822 C 1
chr1 583821554 583821710 Gene3 . -1 -1 . 0
The -wao option writes the original A and B entries plus the number of base pairs of overlap between the two features (which maybe it's useful for you), therefore you'll keep in the output all the information from the input and you'll be able to transform it as you may need.
Your question is not clear enough. Do you just want to annotate your snps in file1 with the information in file2, and does the gtf file refer to the file2 in your example? If that'd the case, file1 and file2 should be the first and the second arguments respectively in the bedtools command:
$ awk 'OFS="\t"{print $1, $2-1, $2, $3}' file1.txt \
| bedtools intersect -a - -b file2.bed -loj | cut -f1,3,4,8
chr1 271353586 T Gene1
chr1 897272822 C Gene2
chr1 913363908 T .
The -loj option performs a “left outer join”: for each feature in A it reports each overlap with B, and a NULL feature for B if no overlaps are found. It's similar to the -wao option but without the uneeded overlap base count.
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