SYNOPSIS

DESCRIPTION

Either outputs summry stats for the list of files, or performs variant calling

Options (later options override earlier):

-s Calculate statistics -v Calculate variants bases on supplied parameters (see -S) -f Reference fasta (required if using bams, ignored otherwise) -m Min locii depth (0) -a Min allele depth (0) -p Min allele pct by quality (0) -q Min qual (3) -Q Min mapping quality (0) -b Min pct balance (strand/total) (0) -D FLOAT Max duplicate read fraction (depth/length per position) (1) -B Turn off BAQ correction (false) -R Homopolymer repeat indel filtering (8) -e FLOAT Alpha filter to use, requires -l or -S (.05) -g FLOAT Global minimum error rate (default: assume phred is ok) -l INT Number of locii in total pileup used for bonferroni (1 mil) -x CHR:POS Output this pos only, then quit -N FIL Output noise stats to FIL -S FIL Read in statistics and params from a previous run with -s (do this!) -A ANNOT Calculate in-target stats using the annotation file (requires -o) -o PREFIX Output prefix (note: overlaps with -N)

Input files

Files must be sorted bam files with bai index files available. Alternatively, a single pileup file can be supplied.

Output files

Varcalls go to stdout. Stats go to stdout, or stderr if varcalling too

If an output prefix is used, files are created as follows:

PREFIX.var

Variant calls in tab delimited 'varcall' format

PREFIX.eav

Variant calls in tab delimited 'ea-var' format

PREFIX.vcf

Variant calls, in vcf format

PREFIX.varsum

Summary of variant calls

PREFIX.tgt

On-target stats detail

PREFIX.tgtsum

Summary of on-target stats

PREFIX.noise

Noise stats detail

Stats Output:

Contains mean, median, quartile information for depth, base quality, read len, mapping quality, indel levels. Also estimates parameters suitable for variant calls, and can be passed directly to this program for variant calls

Filtering Details: