User:Lindenb/Notebook/UMR915/20100618

=mysql= creating a table for the samples

create table sample(      id int unsigned primary key auto_increment,       name varchar(20) unique,       description text,       created datetime,       modified timestamp       ); =SNP calling= filtering on depth( min/max) and Q: minimum RMS mapping quality for SNP

samtools pileup -vcf $(HG18) recal_bwa_rmdup_XXXX1.bam |\ samtools.pl varFilter -d 4 -D 1200 -Q 25 |\ java -jar ~/src/code915/dist/pileupfilter.jar -bed PCCR.bed | wc -l 43209 gunzip -c daily/20100601/for_pierre_010610/vcf_maq_pccr_changed_filters/XXXX1.vcf.gz | wc -l 35784

some filters are missing. OK, now just keep the single nucleotide mutations: (...) | awk -F " " '{if(length($4)==1) print;}' | wc -l 37121

adding filter for the snp quality: samtools pileup -vcf $(HG18) recal_bwa_rmdup_XXXX1.bam | samtools.pl varFilter -d 4 -D 1200 -Q 25 |\ java -jar ~/src/code915/dist/pileupfilter.jar -bed PCCR.bed -min-sq 25 |\ awk -F "       " '{if(length($4)==1) print;}' > jeter.pileup wc jeter.pileup 35286

comparison SS2/my data comm -12: 34187 comm -13: 1569  (uniq to SS2 data) eg: 10:1036884,10:114049332 comm -23: 1099  (uniq to MY data) e.g: 10:101153184,10,101283025

=Comparaison Dindel/samtools= same as yesterday but remove non-PCCR from dindel (update: bug found in my src by SS2)


 * count dindel :1492
 * count samtools :3739
 * uniq dindel :889
 * uniq samtools :3136
 * comm dindel/samtools :603

script was: sh 20100618.sh  cat ${HOME}/daily/20100604/XXXXX_variantCalls.VCF |\ grep -v "#" | awk -F '	' '{if(length($5)!=1 && $7==".") print; }' |\ java -jar /home/lindenb/src/code915/dist/posfilter.jar -db XXX_0809_PCCR.bed |\ cut -d '	' -f 1,2 | sort | uniq > jeter1.txt cat ${HOME}/daily/20100528/indels_samtools_bwa/PCCR/XXXXXXsamtoolsIndel.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