NAME

       varcall - ea-utils: output summry stats or perform variant calling

SYNOPSIS

       varcall <-s|-v> <-f REF> [options] bam1 [bam2...]

DESCRIPTION

       Version: 0.9.632 (BETA)

       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: