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, 13:21, 3 July 2014
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| It takes about 2 mins for each pileup job. | | It takes about 2 mins for each pileup job. |
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− | $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101035.recal.bam > 121101035.recal.pileup & | + | $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101035.recal.bam > $OUT/121101035.recal.pileup & |
− | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101043.recal.bam > 121101043.recal.pileup & | + | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101043.recal.bam > $OUT/121101043.recal.pileup & |
− | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101050.recal.bam > 121101050.recal.pileup & | + | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101050.recal.bam > $OUT/121101050.recal.pileup & |
− | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101052.recal.bam > 121101052.recal.pileup & | + | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101052.recal.bam > $OUT/121101052.recal.pileup & |
− | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101415.recal.bam > 121101415.recal.pileup & | + | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101415.recal.bam > $OUT/121101415.recal.pileup & |
− | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > 121101861.recal.pileup & | + | # $GC/bin/samtools mpileup -q 30 -Q 20 -f $REF/human.g1k.v37.fa -l $HGDP/HGDP_938.bed $BAM/121101861.recal.bam > $OUT/121101861.recal.pileup & |
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| We use -q 30 and -Q 20 to exclude reads that have mapping quality score lower than 30 or base quality score lower than 20. | | We use -q 30 and -Q 20 to exclude reads that have mapping quality score lower than 30 or base quality score lower than 20. |