User:Lindenb/Notebook/UMR915/20101214

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Belgium

samtools pileup -vcf chrXXXXXX.fa sample1.recal.bam | /usr/local/package/samtools-0.1.10/misc/sam2vcf.pl -r chrXXXXXX.fa | wc
  24699  246948 1214723
samtools pileup -vcf chrXXXXXX.fa sample2.recal.bam | /usr/local/package/samtools-0.1.10/misc/sam2vcf.pl -r chrXXXXXXX.fa | wc
  33684  336798 1678389

using non-recalibrated files: 

samtools pileup -vcf chrXXXXXX.fa sample1.bam | /usr/local/package/samtools-0.1.10/misc/sam2vcf.pl -r chrXXXXXX.fa | wc
  27970  279658 1373141
samtools pileup -vcf chrXXXXXX.fa sample2.bam | /usr/local/package/samtools-0.1.10/misc/sam2vcf.pl -rchrXXXXXX.fa | wc
  35725  357208 1777426
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