User:Lindenb/Notebook/UMR915/20101122

20101119        Top        20101123       

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