---
name: "varcall"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/varcall"
---

# varcall(1)

ea-utils: output summry stats or perform variant calling

## 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: