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25 bytes added
, 01:27, 9 December 2014
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| === Step 1: bam --> pileup === | | === Step 1: bam --> pileup === |
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− | $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 | + | $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}.HGDP.pileup |
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− | This step takes 5-6 minutes. | + | This step takes ~1 hour for a genome sequenced at 17X. |
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| === Step 2: pileup --> seq === | | === Step 2: pileup --> seq === |