User:Lindenb/Notebook/UMR915/20100623

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Contents

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
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