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The most common samtools view filtering options are:

• -q N – only report alignment records with mapping quality of at least N (>= N).
• -f 0xXX – only report alignment records where the specified flags XX are all set (are all 1)
  • you can provide the flags in decimal, or as here as hexidecimalhexadecimal
• -F 0xXX – only report alignment records where the specified flags XX are all cleared (are all 0)

Setup

Login to stampede2ls6.tacc.utexas.edu and start an idev session.

idev -p normal -m 180 -A UT-2015-05-18N 1 -NA 1OTH21164 -nr 68CoreNGSday5

Next set up a directory for these exercises, and copy an indexed BAM file there. This is a renamed version of the yeast_pairedend.sort.bam file from our Alignment workflow exercises.

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With all the line wrapping, it looks pretty ugly. Still, you can pick out the CIGAR string in colum column 6. Let's select just that column with cut:

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