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Revision as of 11:09, 20 May 2015
, 11:09, 20 May 2015→Run
=== Step 1: bam --> pileup ===
=== Step 1: bam --> 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
$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
This step takes ~1 hour for a genome sequenced at 17X.
This step takes ~1 hour for a genome sequenced at 17X.
python $LASER/pileup2seq/pileup2seq.py \
python $LASER/pileup2seq/pileup2seq.py \
-m $HGDP/HGDP_938.site \
-m $SSREF/HGDP_938.site \
-o $OUT/ancestry/$SAMPLE.HGDP \
-o $OUT/ancestry/$SAMPLE.HGDP \
$OUT/ancestry/$SAMPLE.HGDP.pileup
$OUT/ancestry/$SAMPLE.HGDP.pileup
This step will take about 5-6 minutes.
This step will take about 5-6 minutes.
$LASER/laser -g $HGDP/HGDP_938.geno -c $HGDP/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP &
$LASER/laser -g $SSREF/HGDP_938.geno -c $SSREF/HGDP_938.RefPC.coord -s $OUT/ancestry/$SAMPLE.HGDP.seq -K 20 -k 4 -M 0.8 -o $OUT/ancestry/$SAMPLE.HGDP &
View the results:
View the results:
