User:Lindenb/Notebook/UMR915/20100623
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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