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Exercise: Use samtools view with -F, -f and -q options to create a BAM with unmapped and low quality (< mq 20) reads removed, and only containing mapped, properly paired, high-quality (mapQ 20+) reads. Call the output file yeast_pe.sort.filt.bam.
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| title | Exercise 3 solutionSolution |
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| language | bash |
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| title | solution |
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cd $SCRATCH/core_ngs/alignment/samtools
module load samtools
samtools view -b -F 0x04 -f 0x2 -q 20 -o yeast_pe.sort.filt.bam yeast_pe.sort.bam |
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You want both the secondary (0x100) and unmapped (0x4) flags to be 0. |
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| title | Exercise 3 solutionSolution |
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| language | bash |
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| title | solution |
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| samtools view -b -F 0x104 -f 0x2 -q 20 -o yeast_pe.sort.filt.bam yeast_pe.sort.bam |
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