User:Lindenb/Notebook/UMR915/20101122

20101119        Top        20101121       

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

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
   
  
  #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 jeter3.vcf