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Revision as of 23:21, 18 June 2014
, 23:21, 18 June 2014→Step 1: bam --> 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 > 121101861.recal.pileup &
We use -q 30 and -Q 20 to remove 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.
=== Step 2: pileup --> seq ===
=== Step 2: pileup --> seq ===
