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Revision as of 10:22, 21 May 2015
, 10:22, 21 May 2015→Step 1: bam --> pileup
=== Step 1: bam --> pileup ===
=== Step 1: bam --> pileup ===
$GC/bin/samtools mpileup -q 30 -Q 20 -f $SSREF/gotcloud.ref/hs37d5.fa -l $SSREF/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.HGDP.pileup
$GC/bin/samtools mpileup -q 30 -Q 20 -f $SSREF/gotcloud.ref/hs37d5.fa -l $SSREF/HGDP/HGDP_938.bed $OUT/bams/${SAMPLE}.recal.bam > $OUT/ancestry/${SAMPLE}.HGDP.pileup
This step takes ~1 hour for a genome sequenced at 17X.
This step takes ~1 hour for a genome sequenced at 17X.
