User:Lindenb/Notebook/UMR915/20100701

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20100630        Top        20100702       


Contents

Compare data dindel/samtools for all samples

 for I in X1????
 do
 gunzip -c XXXXXXXXXXXXXX/${I}_variantCalls.VCF.gz |\
 grep -v "#" | awk -F '	' '{if(length($5)!=1 && $7==".") print; }' |\
 java -jar  posfilter.jar \
   -db XXXXXXXXXXXXXXXXXXX.bed |\
 cut -d '	' -f 1,2 | sort | uniq > jeter1.txt
 
 
 cat XXXXXXXXXXXXXXXXXXX/indels_samtools/bwa/PCCR/*_${I}_*_samtoolsIndel.vcf |\
 grep -v "#" | awk -F '	' '{if(length($5)!=1) print; }' |\
 cut -d '	' -f 1,2 | sort | uniq > jeter2.txt
 echo "=== $I =============================="
 echo -n "$I: count dindel :"
 wc -l jeter1.txt
 echo -n "$I: count samtools :"
 wc -l jeter2.txt
 echo -n "$I: uniq dindel :"
 comm -23 jeter1.txt jeter2.txt | wc -l
 echo -n "$I: uniq samtools :"
 comm -13 jeter1.txt jeter2.txt | wc -l
 echo -n "$I: comm dindel/samtools :"
 comm -12 jeter1.txt jeter2.txt | wc -l
 
 rm jeter1.txt jeter2.txt
 done

results sent to SLS2.

generating input for sift

this time I use the table degtobase to map the degenerate bases in the column 'alt' of variation.

 mysql -N -u root -D umr915 -e 'select V.chrom,V.position+1,1,concat(V.ref,"/",D.base),concat("#",V.id) from variation as V,deg2base as D where ref in ("A","T","G","C") and V.alt=D.symbol'|\
  sed 's/^chr//' | tr "        " "," |\
  split -C 990k - sift_

generating input for pph2

this time I use the table degtobase to map the degenerate bases in the column 'alt' of variation.

 mysql -N -u root -D umr915 -e 'select concat(V.chrom,":",V.position+1),concat(V.ref,"/",D.base) from variation as V,deg2base as D where ref in ("A","T","G","C") and V.alt=D.symbol'

Config Proxy for eclipse

eclipse=> prefs=>Java=>insalled JREs => Edit => default VM args:

 -Dhttp.proxyHost=xxxxxxxxxxxx.prive -Dhttp.proxyPort=xxxx
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