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SeqShop: Ancestry On Your Own Genome, June 2014 (view source)

Revision as of 14:10, 20 June 2014

21 bytes removed ,  14:10, 20 June 2014
→‎Step 1: bam --> pileup
Line 17: Line 17:     
=== Step 1: bam --> pileup ===
 
=== Step 1: bam --> pileup ===
−
mkdir $OUT/ancestry
      
  $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa -l $HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.recal.pileup
 
  $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa -l $HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.recal.pileup
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11054"

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