Hi,

I just translated dbNSFP4 to hg19 using my own script without dbNSFP_sort.pl .

# Copy header 
zcat dbNSFP4.0a_variant.chr1.gz|head -n1 > dbNSFP4_hg19.txt
for file in `ls dbNSFP4.0a_variant.chr*.gz`
do 
    echo "process $file `date`" 
    # switch column 8,9 with 1,2 
    # avoid line without hg19 coordiniate ( $8 != ".") 
    # Be sure hg19 coordinate belong to the same chromosom.( I notice some chr11 in chr17 file )
    zcat $file| grep -v "^#"| awk 'BEGIN{FS="\t";OFS="\t"}$8 != "." && $1==$8 {$1=$8; $2=$9; print $0}' > temp.txt
    # Sort by position . Hint: Use -T option to change /tmp/ directory to store huge data cache 
    sort -k2n temp.txt  >> dbNSFP4_hg19.txt
done

# Compress with bgzip with multithread
echo "compress `date`" 
bgzip -@ 4 dbNSFP4_hg19.txt

echo "Create index `date`" 
tabix -s 1 -b 2 -e 2 -c '#' -S 1 dbNSFP4_hg19.txt.gz

Hi,

I had the same problem. Apparently, when you try to run the script and merge them together into one file. It worked for me when I did it separately for each chromosome and then combining it into one text file. I hope this helps.

Hello!

Sorry for the late reply. This is a very crude way to do it but I will be making a script that incorporates all this and does it in one go.

running it one by one for each chromosome

cat dbNSFP4.0a_variant.chr1 | perl dbNSFP_sort.pl 7 8 > dbNSFP4.0a_chr1_hg19.txt
#find '.' in this directory and concatenate the all the files with this name
find . -type f -name 'dbNSFP4.0a_chr*_hg19.txt' -exec cat {} + >> dbNSFP4.0a_variant_hg19.txt 
head -1 dbNSFP4.0a_variant_hg19.txt >header.txt   #save the header in another file
grep -v "#" dbNSFP4.0a_variant_hg19.txt >dbNSFP4.0a_variant_hg19.2.txt   #for removing multiple headers
rm -f dbNSFP4.0a_variant_hg19.txt #remove multiple files
cat header.txt dbNSFP4.0a_variant_hg19.2.txt >dbNSFP4.0a_variant_hg19.txt #add the header to the file
sort -k1,1 -V -s dbNSFP4.0a_variant_hg19.txt   #sort the file according to the chromosome
# Compress and index
bgzip dbNSFP4.0a_variant_hg19.txt
tabix -s 1 -b 2 -e 2 dbNSFP4.0a_variant_hg19.txt.gz