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.
-
-
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
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing... -
The immune system’s power comes from its genetic diversity, allowing myriad threats to be neutralized through first recognizing foreign antigens. That diversity is also what makes the immune system so difficult to study. Recent advances in sequencing technology and computational biology, however, are giving researchers new tools to understand immune responses and immune-related diseases in greater detail.
This convergence of genetics, immunology, and computation...09-01-2026, 05:41 AM
Comment