User:Lindenb/Notebook/UMR915/20100617

=Cleanup= df -h Sys. de fich. Tail. Occ. Disp. %Occ. Monté sur /dev/mapper/mpath0p1 2,0T  954G  1,1T  48% /GENOTYPAGE rm bwa_*.sam.gz ls bwa_[0-9]*.bam | grep -v sorted | xargs rm  rm bwa_[0-9]*.sai =Compare Dindel/Samtools=

cat ${HOME}/daily/20100604/XXXXXX1_variantCalls.VCF |\ grep -v "#" | awk -F '	' '{if(length($5)!=1 && $7==".") print; }' |\ cut -d '	' -f 1,2 | sort | uniq > jeter1.txt cat ${HOME}/daily/20100528/indels_samtools_bwa/PCCR/1777_XXXXX1_250_166370_samtoolsIndel.vcf |\ grep -v "#" | awk -F '	' '{if(length($5)!=1) print; }' |\ cut -d '	' -f 1,2 | sort | uniq > jeter2.txt echo -n "count dindel :" wc -l jeter1.txt echo -n "count samtools :" wc -l jeter2.txt echo -n "uniq dindel :" comm --check-order -23 jeter1.txt jeter2.txt | wc -l echo -n "uniq samtools :" comm --check-order -13 jeter1.txt jeter2.txt | wc -l echo -n "comm dindel/samtools :" comm --check-order -12 jeter1.txt jeter2.txt | wc -l rm jeter1.txt jeter2.txt

=/dev/*=
 * count dindel :9648 jeter1.txt
 * count samtools :3739 jeter2.txt
 * uniq dindel :9039
 * uniq samtools :3130
 * comm dindel/samtools :609

cat /dev/zero | tr "\0" "\n" | cat -n | head -n 100 echo "test-full" > /dev/full =mysql= creating a DB to load the exome bed data. create database umr915; use umr915; create table baitlibrary (id int unsigned primary key auto_increment,name varchar(50) not null,description mediumtext,created datetime not null,modified timestamp); insert into baitlibrary(id,name,description,created,modified) values( #### CANCEL, I don't really need this. Because samtools pileup use a list of discrete positions (not a segment/range)

=configuring SVN for server 2=

edit ~/.subversion/servers

[groups] googlegroup = *.googlecode.com sourceforgegroup= *.sourceforge.net (...) [googlegroup] http-proxy-host=xxxxxxxxxxx http-proxy-port=XXXX [sourceforgegroup] http-proxy-host=XXXXXXXXX http-proxy-port=XXX

=PileupFilter= wrote PileupFilter http://code.google.com/p/code915/source/browse/trunk/tools/src/java/fr/inserm/umr915/tools/PileupFilter.java

ant pileupfilter

test: samtools pileup -vcf ${HG18} recal_bwa_rmdup_XXXX.bam |\ java -jar ~/src/code915/dist/pileupfilter.jar -bed CCR.bed -min-coverage 4 -max-coverage 1200 |\ wc -l