Question: .dict file created by picard and by samtools
5
gravatar for haiying.kong
3.8 years ago by
haiying.kong290
Germany
haiying.kong290 wrote:

There are 2 ways of generating .dict file for human genome.

java -jar picard.jar CreateSequenceDictionary REFERENCE=reference.fa OUTPUT=reference.dict

samtools faidx ref.fasta

I found that the 2 files generated in the 2 different command have different file size.

I need .dict file for GATK and Picard. Which one is correct one?

Thank you very much.

next-gen • 12k views
ADD COMMENTlink modified 2.2 years ago by Bioinfonext150 • written 3.8 years ago by haiying.kong290
1

The files created by both the tools are different. I guess u need both .fai and .dict to use .fa as a reference 

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by geek_y9.7k

I am not able to understand how to create a dictionary by using the latest version of Picard 2.8.1.

It is different from the previous version.

Should I use i for input instead of REFERENCE and what will be option for output?

Old Picard 1.8.1 Command:

jar /home/yog/software/picard-2.8.1/src/main/java/picard/sam/CreateSequenceDictionary.java REFERENCE=R1_R9.fasta OUTPUT=R1_R9.dict

New Command options:

 jar /home/yog/software/picard-2.8.1/src/main/java/picard/sam/CreateSequenceDictionary.java

Illegal option: /

Usage: jar {ctxui}[vfmn0PMe] [jar-file] [manifest-file] [entry-point] [-C dir] files ... Options:

-c  create new archive

-t  list table of contents for archive

-x  extract named (or all) files from archive

-u  update existing archive

-v  generate verbose output on standard output

-f  specify archive file name

-m  include manifest information from specified manifest file

-e  specify application entry point for stand-alone application

    bundled into an executable jar file

-0  store only; use no ZIP compression

-P  preserve leading '/' (absolute path) and ".." (parent directory) components from file names

-M  do not create a manifest file for the entries

-i  generate index information for the specified jar files

-C  change to the specified directory and include the following file
ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by Bioinfonext150
8
gravatar for igor
3.8 years ago by
igor7.7k
United States
igor7.7k wrote:

Picard CreateSequenceDictionary creates .dict file and samtools faidx creates a .fai file. Both are needed for GATK.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by igor7.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2078 users visited in the last hour