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Revision as of 13:24, 18 June 2014
, 13:24, 18 June 2014→Preparing input files for LASER
It takes about 2 mins for each pileup job.
It takes about 2 mins for each pileup job.
$GC/bin/samtools mpileup -q 30 -Q 20 -f ./reference/hs37d5.fa.rz -l ./HGDP/HGDP_938.bed ./BAM/121101035.recal.bam > 121101035.recal.pileup &
$GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101035.recal.bam > 121101035.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f ./reference/hs37d5.fa.rz -l ./HGDP/HGDP_938.bed ./BAM/121101043.recal.bam > 121101043.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101043.recal.bam > 121101043.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f ./reference/hs37d5.fa.rz -l ./HGDP/HGDP_938.bed ./BAM/121101050.recal.bam > 121101050.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101050.recal.bam > 121101050.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f ./reference/hs37d5.fa.rz -l ./HGDP/HGDP_938.bed ./BAM/121101052.recal.bam > 121101052.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101052.recal.bam > 121101052.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f ./reference/hs37d5.fa.rz -l ./HGDP/HGDP_938.bed ./BAM/121101415.recal.bam > 121101415.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101415.recal.bam > 121101415.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f ./reference/hs37d5.fa.rz -l ./HGDP/HGDP_938.bed ./BAM/121101861.recal.bam > 121101861.recal.pileup &
# $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/hs37d5.fa.rz -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > 121101861.recal.pileup &
Step 2: pileup --> seq
Step 2: pileup --> seq
