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21 bytes added
, 14:08, 20 June 2014
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| === Step 1: bam --> pileup === | | === Step 1: bam --> pileup === |
| + | mkdir $OUT/ancestry |
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| $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 |