EnglishFrenchSpanish

OnWorks favicon

varcall - Online in the Cloud

Run varcall in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command varcall that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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:

Use varcall online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Image Downloader
    Image Downloader
    Crawl and download images using
    Selenium Using python3 and PyQt5.
    Supported Search Engine: Google, Bing,
    Baidu. Keywords input from the keyboard
    or input from ...
    Download Image Downloader
  • 2
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    discussio...
    Download Eclipse Tomcat Plugin
  • 3
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 4
    GenX
    GenX
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 5
    pspp4windows
    pspp4windows
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 6
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • More »

Linux commands

Ad