[ekg]

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.

[Soumya18]

Need more information!

Dear All,

Could you please let me know what is rangehg18.chr?

You can force samtools mpileup with pipe to bcftools to produce lots'o'info like this ...

samtools mpileup -R -d 1000 -l rangehg18.chr -uf hg18.fa in.bam | bcftools view -g - > out.vcf

Note the -g parameter, it forces calls and outputs for all locations.
Check why you're not getting calls in the details of the VCF file.
You can write your own caller based on the VCF information if you need to.

[Richard Finney]

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 ]