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, 11:09, 20 May 2015
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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}.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 |
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| This step takes ~1 hour for a genome sequenced at 17X. | | This step takes ~1 hour for a genome sequenced at 17X. |
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| 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 |
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| This step will take about 5-6 minutes. | | This step will take about 5-6 minutes. |
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− | $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 & |
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| View the results: | | View the results: |