User:Lindenb/Notebook/UMR915/20100623

=48H00= export SVG to PNG (150 dpi): inkscape -f slide_001.svg -z -d 150 --export-png=slide_001.png =mysql/variation= changed source: i will store the 0-based position instead of the 1-based position: easier to join with ucsc data:

update variation set position=position-1; =inserting sls2's data= cf; ~/dail/20100623:

for I in XX1 XX2 XX3 XX4 XX5 XX6 XX7 XX8 XX9 XX10 do       echo $I for F in `find /GENOTYPAGE/data/project/20100603_solena/Iomega_HDD/variants/snps_changed_filters/ -name "*.vcf" | grep "_${I}_"` do               echo " $F" ${HOME}/bin/insertvariants.sh -s "$I" -t vcf -d "$F" $F done done =indexing the recalibrated files= for F in recal_bwa_rmdup_XXX*.bam ; do samtools index $F ; done =Running pileup= for I in XX1 ... do 	echo "$I" samtools pileup -vcf ${HG18} recal_bwa_rmdup_${I}.bam |\ java -jar ~/src/code915/dist/pileupfilter.jar \ -bed xxxPCCR.bed |\ gzip --best > recal_bwa_rmdup_${I}.pileup.gz  done