novoalign -o SAM -F ILMFQ -t120 -r0.2 -q5 -d hg19.ndx -f 7746x2_s_6_1_sequence.txt.gz 7746x2_s_6_2_sequence.txt.gz | grep chr > 7746x2.sam
samtools view -bS 7746x2.sam | samtools sort - 7746x2
samtools rmdup 7746x2.bam 7746x2.sorted.bam
samtools index 7746x2.sorted.bam
samtools view -u -q 20 7746x2.sorted.bam | samtools pileup -vcf /DataDisk/Analysis/Sun/fa/hg19/chr1.fa - | samtools.pl varFilter -D 100 -G 50 > 1.var
awk '($3=="*"&&$6>=50)||($3!="*"&&$6>30)' 1.var > 1.var.filtered
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