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: