User:Lindenb/Notebook/UMR915/20101006

=Charpak= continue dev. http://code.google.com/p/code915/source/detail?r=269

created a nice jsp custom tag looking into Wikipedia



=Testing Varscan= samtools pileup -f hg18/chr1.fa chr1.sorted.bam > chr1.pileup

pileup2snp
java -jarVarScan.v2.2.2.jar pileup2snp chr1.pileup > chr1.varscan

head -n 3 chr1.varscan | java -jar verticalize.jar | sed 's/^/  /' >>2 $1 Chrom : chr1 $2 Position : 51 $3 Ref : A $4 Var : C  $5 Reads1 : 185 $6 Reads2 : 2 $7 VarFreq : 1.07% $8 Strands1 : 2 $9 Strands2 : 1 $10 Qual1 : 32 $11 Qual2 : 30 $12 Pvalue : 0.98 $13 MapQual1 : 1 $14 MapQual2 : 1 $15 Reads1Plus : 119 $16 Reads1Minus : 66 $17 Reads2Plus : 0 $18 Reads2Minus : 2 $19 ? : C <<2 >>3 $1 Chrom : chr1 $2 Position : 53 $3 Ref : C $4 Var : T  $5 Reads1 : 231 $6 Reads2 : 5 $7 VarFreq : 2.12% $8 Strands1 : 2 $9 Strands2 : 2 $10 Qual1 : 33 $11 Qual2 : 33 $12 Pvalue : 0.98 $13 MapQual1 : 1 $14 MapQual2 : 1 $15 Reads1Plus : 156 $16 Reads1Minus : 75 $17 Reads2Plus : 2 $18 Reads2Minus : 3 $19 ? : T <<3

pileup2indel
java -jarVarScan.v2.2.2.jar pileup2indel chr1.pileup > chr1.varscan

head -n 3 chr1.varscan | java -jar /home/lindenb/src/lindenb/build/verticalize.jar | sed 's/^/  /' >>2 $1 Chrom : chr1 $2 Position : 439 $3 Ref : A $4 Var : -C $5 Reads1 : 8 $6 Reads2 : 2 $7 VarFreq : 20% $8 Strands1 : 2 $9 Strands2 : 1 $10 Qual1 : 30 $11 Qual2 : 26 $12 Pvalue : 0.98 $13 MapQual1 : 1 $14 MapQual2 : 1 $15 Reads1Plus : 4 $16 Reads1Minus : 4 $17 Reads2Plus : 0 $18 Reads2Minus : 2 $19 ? : DEL-1-C <<2 >>3  $1 Chrom : chr1 $2 Position : 2737 $3 Ref : C $4 Var : -T $5 Reads1 : 20 $6 Reads2 : 2 $7 VarFreq : 9.09% $8 Strands1 : 2 $9 Strands2 : 1 $10 Qual1 : 33 $11 Qual2 : 33 $12 Pvalue : 0.98 $13 MapQual1 : 1 $14 MapQual2 : 1 $15 Reads1Plus : 16 $16 Reads1Minus : 4 $17 Reads2Plus : 2 $18 Reads2Minus : 0 $19 ? : DEL-1-T <<3