User:Lindenb/Notebook/UMR915/20110225

20110225        Top        20110228       

Problem with "Variation predictor:" answer from the dev mailing list: see http://lists.ensembl.org/pipermail/dev/2011-February/000928.html

Submitting each SNP after each SNP :-( UGLY

rm -f merged_result.vcf
cat   ${HOME}/sample1.hg19.vcf ${HOME}/sample2.hg19.vcf | cut -d '	' -f 1-5
 | grep -v "#" | sort | uniq > jeter.vcf
while read line
do
	echo "$line"
	echo $line | ./variant_effect_predictor.pl --format vcf -o jeter.variant
.txt --hgnc --check_ref
	cat  jeter.variant.txt | grep -v "Uploaded Variation" >> merged_result.v
cf
	rm jeter.variant.txt
done < jeter.vcf