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

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/ REFERENCE=R1_R9.fasta OUTPUT=R1_R9.dict

New Command options:

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

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
gravatar for igor
3.8 years ago by
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
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