User:Lindenb/Notebook/UMR915/20101122

Cedric/Integragen
coverage exon ?

/usr/local/package/bwa-0.5.7/bwa index -a is exon.fa /usr/local/package/bwa-0.5.7/bwa aln  -l 32 -q 15 -t 10  -fexon1.aln exon.fa s_5_1_sequence.txt /usr/local/package/bwa-0.5.7/bwa aln -l 32 -q 15 -t 10  -fexon2.aln exon.fa s_5_2_sequence.txt /usr/local/package/bwa-0.5.7/bwa sampe -a 600 exon.fa exon1.aln exon2.aln  s_5_1_sequence.txt s_5_2_sequence.txt  >  sampe.sam /usr/local/package/samtools-0.1.10/samtools sort sampe.bam sampe.sort /usr/local/package/samtools-0.1.10/samtools index sampe.sorted.bam /usr/local/package/samtools-0.1.10/samtools pileup -c -v -f mygene.fa sampe.sorted.bam ##EMPTY RESULT

Belgium
samtools faidx chrX1_X2.fa  bin/freebayes --fasta-reference /GENOTYPAGE/data/users/lindenb/20101108_belgium/chrX1_X2.fa -i /GENOTYPAGE/data/users/lindenb/20101108_belgium/jeter.bam > FreeBayes.sample1.vcf /usr/local/package/samtools-0.1.10/samtools pileup -f chrX1_X2.fa jeter.bam | java -jar /usr/local/package/varscan/VarScan.v2.2.jar pileup2snp > VarScanSnp.sample1.tsv /usr/local/package/samtools-0.1.10/samtools pileup -f chrX1_X2.fa jeter.bam | java -jar /usr/local/package/varscan/VarScan.v2.2.jar pileup2indel > VarScanIndels.sample1.tsv java -jar /usr/local/package/gatk/GenomeAnalysisTK-1.0.4705/GenomeAnalysisTK.jar -T UnifiedGenotyper -R chrX1_X2.fa -I jeter.bam --DBSNP  /GENOTYPAGE/data/pubdb/broad.mit.edu/gsa/resources/dbsnp_130_hg18.rod -o jeter4.vcf /usr/local/package/samtools-0.1.10/samtools pileup -v -c -f chrX1_X2.fa jeter.bam | python /usr/local/package/samtools-0.1.10/misc/varfilter.py -D 100 > Samtools.pileup.sample1.vcf #no result with java -jar /usr/local/package/gatk/GenomeAnalysisTK-1.0.4705/GenomeAnalysisTK.jar -T IndelGenotyperV2 -R chrX1_X2.fa -I jeter.bam  -bed jeter.bed -verbose jeter2.txt -o GatkUnifiedGenotyper.sample1.vcf

24301 jeter.freebayes.sample1.txt 2986 jeter.gatk.txt 10937 jeter.pileup.samtools.txt 19509 jeter.varscan.txt 8930 jeter.clc.sampl1.txt

for I in jeter*txt; do for J in jeter*txt; do echo -n $I "      " $J "  " ; comm -1 -2 $I $J | wc -l ; done; done

jeter.freebayes.sample1.txt     jeter.gatk.txt         1838 jeter.freebayes.sample1.txt     jeter.pileup.samtools.txt      3029 jeter.freebayes.sample1.txt     jeter.varscan.txt      5486 jeter.gatk.txt  jeter.freebayes.sample1.txt    1838 jeter.gatk.txt  jeter.pileup.samtools.txt      2354 jeter.gatk.txt  jeter.varscan.txt      1871 jeter.pileup.samtools.txt       jeter.freebayes.sample1.txt    3029 jeter.pileup.samtools.txt       jeter.gatk.txt         2354 jeter.pileup.samtools.txt       jeter.varscan.txt      4642 jeter.varscan.txt       jeter.freebayes.sample1.txt    5486 jeter.varscan.txt       jeter.gatk.txt         1871 jeter.varscan.txt       jeter.pileup.samtools.txt      4642

jeter.clc.samp1e1.txt jeter.freebayes.sample1.txt   2336 jeter.clc.sample1.txt jeter.pileup.samtools.txt   2192 jeter.clc.sample1.txt jeter.varscan.txt   2051 jeter.clc.sample1.txt jeter.gatk.txt   2067