CallSam

SYNOPSIS

CallSam is intended to be a simple base caller based on majority rules
and level of depth. It is also intended to be a base caller for every
site in the bam file. However, the user can choose to see only
variant sites by specifying --variants-only.

CallSam is fast because it is multithreaded. However due to thread
race conditions, the base calls could be unsorted. Internally,
CallSam sorts the VCF on position before outputting it unless the 
user specifies the --unsorted flag.  Sorting is moot if only one
cpu is being used and so --unsorted is set internally if only one
cpu is specified. One cpu is the default.

AUTHOR
Lee Katz <lkatz@cdc.gov>

INSTALLATION
Copy the perl script to a bin directory in your path

USAGE

Creates a vcf from a sorted bam file.
  Usage: callsam.pl file.sorted.bam > out.vcf
  --min-coverage 10 Min depth at a position
  --min-frequency 0.75 Min needed for majority
  -ref reference.fasta (optional)
  --numcpus 1
  --unsorted Produces streaming output, but unsorted due to thread race conditions
  --variants-only Do not print invariant sites
  -mpileup '-q 1' Send options to mpileup 'samtools mpileup' for additional help

EXAMPLES

# very conservative
callsam.pl file.sorted.bam --min-coverage 20 --min-frequency 1 > out.vcf
# even more conservative with an mpileup parameter
callsam.pl file.sorted.bam --min-coverage 20 --min-frequency 1 -mpileup '-q 20' > out.vcf

# fast
callsam.pl file.sorted.bam --numcpus 12 --unsorted > out.vcf
# fast and smaller, more targeted vcf file
callsam.pl file.sorted.bam --numcpus 12 --unsorted --variants-only > out.vcf

# Sort it yourself, not using internal sorting.
callsam.pl file.sorted.bam --unsorted | sort -k1,1 -k2,2n > out.vcf