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Revision as of 12:39, 19 June 2014
, 12:39, 19 June 2014→Step 2: pileup --> seq
=== Step 2: pileup --> seq ===
=== Step 2: pileup --> seq ===
python $LASER/pileup2seq/pileup2seq.py \
python $LASER/pileup2seq/pileup2seq.py \
-m $HGDP/HGDP_938.site \
-m $HGDP/HGDP_938.site \
-o $OUT/ancestry/$SAMPLE.laser \
-o $OUT/ancestry/$SAMPLE.laser \
$OUT/bams/${SAMPLE}.recal.bam
$OUT/bams/${SAMPLE}.recal.bam
=== Estimate ancestry ===
=== Estimate ancestry ===
$LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.laser.seq -K 20 -k 4 -x 1 -y 3 -o $OUT/ancestry/$SAMPLE.laser.1 &
$LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.laser.seq -K 20 -k 4 -x 1 -y 3 -o $OUT/ancestry/$SAMPLE.laser.1 &
