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Old 05-30-2011, 12:06 PM   #1
Sylphide
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Default SAM/BAM how to retrieve all mapped reads ?

Hello,
I obtained a BAM file from BWA and would like to keep only mapped reads. Samtools view -q 1 removes reads with mapQ 0 and I would like to conserve them.
Does anyone have a solution ?
Many thanks

Last edited by Sylphide; 05-30-2011 at 12:39 PM.
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Old 05-30-2011, 06:14 PM   #2
nilshomer
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samtools view -F 4

See: http://picard.sourceforge.net/explain-flags.html
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Old 05-31-2011, 06:57 AM   #3
prisnirath
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Hi...
I used BWA to get a sam file and used SamTools to call the variants in my reads, got huge no. of variants.
Whe I viewed my sam file using tablet app., I got hold of datasets showing variants with read depth 1.
how do I manipulate the read depth and set its min. value to be around 50 or so to call in genuine SNPs?
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