.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH VARCALL "1" "July 2015" "varcall 1.1.2" "User Commands"
.SH NAME
varcall \- ea-utils: output summry stats or perform variant calling
.SH SYNOPSIS
.B varcall
\fI\,<-s|-v> <-f REF> \/\fR[\fI\,options\/\fR] \fI\,bam1 \/\fR[\fI\,bam2\/\fR...]
.SH DESCRIPTION
Version: 0.9.632 (BETA)
.PP
Either outputs summry stats for the list of files, or performs variant calling
.PP
Options (later options override earlier):
.PP
\fB\-s\fR          Calculate statistics
\fB\-v\fR          Calculate variants bases on supplied parameters (see \fB\-S\fR)
\fB\-f\fR          Reference fasta (required if using bams, ignored otherwise)
\fB\-m\fR          Min locii depth (0)
\fB\-a\fR          Min allele depth (0)
\fB\-p\fR          Min allele pct by quality (0)
\fB\-q\fR          Min qual (3)
\fB\-Q\fR          Min mapping quality (0)
\fB\-b\fR          Min pct balance (strand/total) (0)
\fB\-D\fR FLOAT    Max duplicate read fraction (depth/length per position) (1)
\fB\-B\fR          Turn off BAQ correction (false)
\fB\-R\fR          Homopolymer repeat indel filtering (8)
\fB\-e\fR FLOAT    Alpha filter to use, requires \fB\-l\fR or \fB\-S\fR (.05)
\fB\-g\fR FLOAT    Global minimum error rate (default: assume phred is ok)
\fB\-l\fR INT      Number of locii in total pileup used for bonferroni (1 mil)
\fB\-x\fR CHR:POS  Output this pos only, then quit
\fB\-N\fR FIL      Output noise stats to FIL
\fB\-S\fR FIL      Read in statistics and params from a previous run with \fB\-s\fR (do this!)
\fB\-A\fR ANNOT    Calculate in\-target stats using the annotation file (requires \fB\-o\fR)
\fB\-o\fR PREFIX   Output prefix (note: overlaps with \fB\-N\fR)
.PP
Input files
.PP
Files must be sorted bam files with bai index files available.  Alternatively,
a single pileup file can be supplied.
.PP
Output files
.PP
Varcalls go to stdout.  Stats go to stdout, or stderr if varcalling too
.SS "If an output prefix is used, files are created as follows:"
.TP
PREFIX.var
Variant calls in tab delimited 'varcall' format
.TP
PREFIX.eav
Variant calls in tab delimited 'ea\-var' format
.TP
PREFIX.vcf
Variant calls, in vcf format
.TP
PREFIX.varsum
Summary of variant calls
.TP
PREFIX.tgt
On\-target stats detail
.TP
PREFIX.tgtsum
Summary of on\-target stats
.TP
PREFIX.noise
Noise stats detail
.PP
Stats Output:
.PP
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
.PP
Filtering Details: