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Revision as of 01:46, 8 December 2014
, 01:46, 8 December 2014→Step 1: bam --> pileup
=== Step 1: bam --> pileup ===
=== Step 1: bam --> 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
$GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.recal.pileup
This step takes 5-6 minutes.
This step takes 5-6 minutes.
