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.dict file created by picard and by samtools

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
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updated by Ram Ram • written by haiying.kong haiying.kong

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

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updated by Ram Ram • written by GouthamAtla GouthamAtla

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
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updated by Ram Ram • written by Bioinfonext Bioinfonext

1 answer

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

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written by igor igor

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