User:Lindenb/Notebook/UMR915/20101019
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Mediawiki
allow file permission for upload
sudo chown -R apache: images
Exome Explorer
working on a BDB based solution for exploring the exome data.
inserting varscan data computed last week:
for I in 1 ...
do
echo $I
java -jar exomeexplorer.jar -dataset Brs -p varscan -sample-id ${I} ~/tmp/varscan_pileup2indel_${I}.tsv.gz
done
for I in 1 ...
do
echo $I
java -jar exomeexplorer.jar -dataset Brs -p varscan -sample-id ${I} ~/tmp/varscan_pileup2snp_${I}.tsv.gz
done
size:
du -h ${BDB_HOME}
913M
export to PPH2
java -jar /home/lindenb/src/code915/dist/exomeexplorer.jar -dataset BRUGADA -p export-pph2 | grep -v random | cut -d ':' -f 1 | uniq -c 282162 chr1 167581 chr10 133953 chr11 124379 chr12 43800 chr13 70688 chr14 100045 chr15 132123 chr16 133673 chr17 52556 chr18 131116 chr19 206142 chr2 60017 chr20 47914 chr21 54993 chr22 136773 chr3 178806 chr4 113768 chr5 125006 chr6 141257 chr7 94362 chr8 118050 chr9 489 chrM 70106 chrX 106560 chrY
same number as in varscan ?
gunzip -c ~/tmp/varscan_pileup2snp_*.gz | grep -v random | grep -v Chrom | cut -d ' ' -f 1,2,3,4 | sort | uniq | cut -d ' ' -f 1 | sort | uniq -c
282162 chr1 167581 chr10 133953 chr11 124379 chr12 43800 chr13 70688 chr14 100045 chr15 132123 chr16 133673 chr17 52556 chr18 131116 chr19 206142 chr2 60017 chr20 47914 chr21 54993 chr22 136773 chr3 178806 chr4 113768 chr5 125006 chr6 141257 chr7 94362 chr8 118050 chr9 489 chrM 70106 chrX 106560 chrY
ok same
