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It appears that samtools is not using reads which are not marked as proper pairs. This was my problem, and it led me to this thread. I fixed it with bamtools resolve.
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The "-l parameter " (i.e. "dash el") specifies a file of (genomic postions) OR (genomic ranges in bed format) to produce output for. Regions OR positions not specified are dropped (not produced in output, i.e. "skipped").
typing "samtools mpileup" on the command line provides information on all the parameters appropriate to the "mpileup" feature of samtools.
bash-3.2$ samtools mpileup
Usage: samtools mpileup [options] in1.bam [in2.bam [...]]
Input options:
-6, --illumina1.3+ quality is in the Illumina-1.3+ encoding
... [ deleted stuff ]
-G, --exclude-RG FILE exclude read groups listed in FILE
-l, --positions FILE skip unlisted positions (chr pos) or regions (BED)
... [ deleted stuff ]Comment
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