User:Lindenb/Notebook/UMR915/20100616

=Downloading Resources for GATK= mkdir -p /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa cd /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa export ftp_proxy=########### wget ftp://ftp.broad.mit.edu/pub/gsa/gatk_resources.tgz tar xvfz gatk_resources.tgz resources/ resources/dbsnp_130_b37.rod resources/Homo_sapiens_assembly18.fasta resources/human_g1k_v37.dict resources/human_b36_both.fasta resources/human_g1k_v37.fasta resources/dbsnp_130_b36.rod resources/dbsnp_129_hg18.rod resources/dbsnp_129_b36.rod resources/human_b36_both.dict resources/Homo_sapiens_assembly18.fasta.fai resources/Homo_sapiens_assembly18.dict resources/human_g1k_v37.fasta.fai resources/human_b36_both.fasta.fai resources/dbsnp_130_hg18.rod rm gatk_resources.tgz

GATK -T CountCovariates requires that the BAM was indexed.

=CountCovariates= as defined at http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration first test with java -Xmx4g -jar /usr/local/package/gatk/GenomeAnalysisTK-1.0.3471/GenomeAnalysisTK.jar \ -l INFO -R /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/Homo_sapiens_assembly18.fasta \ --DBSNP /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/dbsnp_129_hg18.rod \ -I bwa_rmdup_XXXXXXXXXXXXXX.bam \ -T CountCovariates \ -cov ReadGroupCovariate \ -cov QualityScoreCovariate \ -cov CycleCovariate \ -cov DinucCovariate \ -recalFile my_reads.recal_data.csv \ --default_platform illumina

content of my_read.recal_data.csv

# Counted Sites   960945769 # Counted Bases   8925331332 # Skipped Sites   3899696 # Fraction Skipped 1 / 246 bp ReadGroup,QualityScore,Cycle,Dinuc,nObservations,nMismatches,Qempirical bwa_rmdup_XXXXX.bam,2,-54,AA,254,143,2 bwa_rmdup_XXXXX.bam,2,-54,AC,111,40,4 bwa_rmdup_XXXXX.bam,2,-54,AG,91,39,4 bwa_rmdup_XXXXX.bam,2,-54,AT,118,36,5 bwa_rmdup_XXXXX.bam,2,-54,CA,289,11,14 bwa_rmdup_XXXXX.bam,2,-54,CC,696,642,1 bwa_rmdup_XXXXX.bam,2,-54,CG,100,24,6 (...)

TableRecalibration
option -nt (num thread) doesn't work here.

java -Xmx4g -jar /usr/local/package/gatk/GenomeAnalysisTK-1.0.3471/GenomeAnalysisTK.jar \ -l INFO \ -R /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/Homo_sapiens_assembly18.fasta \ -I bwa_rmdup_XXXX.bam \ -T TableRecalibration \ -outputBam jeter.bam \ -recalFile my_reads.recal_data.csv \ --default_platform illumina

=Mysql= yum install mysql-server.x86_64 mkdir -p /GENOTYPAGE/data/mysql/datadir

current content of /etc/my.cnf is

[mysqld] datadir=/var/lib/mysql socket=/var/lib/mysql/mysql.sock user=mysql # Default to using old password format for compatibility with mysql 3.x # clients (those using the mysqlclient10 compatibility package). old_passwords=1 # Disabling symbolic-links is recommended to prevent assorted security risks; # to do so, uncomment this line: # symbolic-links=0 [mysqld_safe] log-error=/var/log/mysqld.log pid-file=/var/run/mysqld/mysqld.pid

permission for /var/lib/mysql ls -la /var/lib/mysql total 12 drwxr-xr-x 2 mysql mysql 4096 mai 20 16:24.

changing permissions: cd /GENOTYPAGE/data/mysql chown mysql:mysql datadir ls -la total 12 drwxr-xr-x 3 root root  4096 jun 16 11:29. drwxr-xr-x 6 root root  4096 jun 16 11:29 .. drwxr-xr-x 2 mysql mysql 4096 jun 16 11:29 datadir

editing datadir in /etc/my.cnf #datadir=/var/lib/mysql datadir=/GENOTYPAGE/data/mysql/datadir

starting mysql /etc/init.d/mysqld start Initialisation de la base de données MySQL : Installing MySQL system tables... OK Filling help tables... OK To start mysqld at boot time you have to copy support-files/mysql.server to the right place for your system (...) Démarrage de MySQL :                                       [  OK  ] =ADE4 for R= install.packages('ade4')