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Old 04-25-2016, 05:42 AM   #1
cwwang
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Location: Wuhan of China

Join Date: Apr 2016
Posts: 1
Post Help samtools view -q option

Hi,I want to know what's the realitionship between the' samtools view -q option'
and the score in the corresponding bed file,and their biological meaning .
I used the following command:
"bwa mem -t 4 ref.fa t_1.fq t_2.fq|samtools view -bS -q 30 -|bamToBed >t.bed"
It seems that when I set the samtools view option "-q 30",all the score value in the t.bed are greater than 30,just like the fllowing show:
"chr13 46697 46787 FCC0AA0ACXX:2:1105:17795:189664#GCGACTCC/1 40 +
chr13 47041 47131 FCC0AA0ACXX:2:1105:17795:189664#GCGACTCC/2 47 -"
My fastq files are about DNA seq reads,it has been said the '-q' in samtools view is about mapping quality.
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