Snps annotation Post: 302990583

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Top Forums UNIX for Beginners Questions & Answers Snps annotation Post 302990583 by marwah on Saturday 28th of January 2017 09:35:05 PM

01-28-2017

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Snps annotation

I have the following Snps data

Code:

 CHROM	POS	ID
chr7	78599583	rs987435
chr15	33395779	rs987436
chr1	189807684	rs987437
chr20	33907909	rs987438
chr12	75664046	rs987439

and the following gene data

Code:

genename    name    chrom   strand  txstart txend
MAGI2	NM_001301128	chr7	-	77484309	78920826	77486567	78920572	21
MRPS18C	NM_001297769	chr4	+	84596108	84601900	84596254	84601206	5
MRPS18C	NM_001297767	chr4	+	84596108	84601900	84596254	84601374	5
GCOM1	NM_001018091	chr15	+	55671393	55797047	55671524	55794059	13
FAHD1	NM_001018104	chr16	+	1817225	1830204	1817231	1828128	3
FAM134B	NM_001034850	chr5	-	16526146	16670167	16527849	16670080	9

I'm trying to find the snp whose postion (POS) lie between the txstart and txend in the gene data
so for this data I have the first SNP will lie between MAGI2 txstart and txend

the out put should be

Code:

gene      ID        CHROM  POS       txstart      txend
MAGI2 rs987435 chr7 78599583 77484309 78920826

I have tried the following but it didn't work

Code:

awk '
FNR==1 {next}
FNR == NR {
        POS[++k]=$1
        ID[k]=$2
        next
}
{       for(i = 1; i <= k; i++)
                if(POS[i]>=$5 && POS[i]<=$6)
                        print $1, ID[i], $3, POS[i], $5, $6
}' pre_snpinfo_tumor.txt  refFlat.txt

snps data= pre_snoinfo_tumor.txt
gene dat=refFlat.txt

Last edited by marwah; 01-29-2017 at 05:10 AM..

marwah

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