User:Lindenb/Notebook/UMR915/20100617

20100616        Top        20100618       

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

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

/dev/*

 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