User:Lindenb/Notebook/UMR915/20100701
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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
