User:Lindenb/Notebook/UMR915/20100701

=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