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Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Problem with PICARD FilterVcf

Dear all,
I have a problem using Picard tool FilterVcf.
I first run the command:

java -jar picard.jar FilterVcf \
MIN_AB=10.0 \
INPUT=12-3455_S6.final.vcf \
OUTPUT=test.vcf

And I receive the error:

[Mon Aug 31 12:04:53 CEST 2015] Executing as smerella@b002 on Linux 2.6.32-279.2.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18; Picard version: 1.138() JdkDeflater
[Mon Aug 31 12:04:56 CEST 2015] picard.vcf.filter.FilterVcf done. Elapsed time: 0.06 minutes.
Runtime.totalMemory()=1138753536
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.IllegalArgumentException: A reference dictionary is required for creating Tribble indices on the fly
at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:389)
at picard.vcf.filter.FilterVcf.doWork(FilterVcf.java:97)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

Then I tried with:
java -jar picard.jar FilterVcf \
REFERENCE_SEQUENCE=/lustre1/genomes/hg19/fa/hg19 \
MIN_AB=10.0 \
INPUT=12-3455_S6.final.vcf \
OUTPUT=test.vcf

And I received the same error. In the directory /lustre1/genomes/hg19/fa/ I have the files hg19.dict hg19.fa hg19.fa.fai.
I don't understand what I am doing wrong.

Thanks for the help.

[smerella@b002 scratch_bmc]$ java -jar picard.jar FilterVcf --version
1.138()

Issue · Github
by Sheila

Issue Number
147
State
closed
Last Updated
Milestone
Array
Closed By
chandrans

Best Answer

Answers

  • SheilaSheila Broad InstitutePosts: 4,858 admin

    @merella.stefania
    Hi,

    Your input reference does not have the .fa ending. Try with hg19.fa instead of hg19

    -Sheila

  • merella.stefaniamerella.stefania ItalyPosts: 28

    Dear Sheila,
    thanks for the answer!! I tried with:

    java -jar picard.jar FilterVcf REFERENCE_SEQUENCE=/lustre1/genomes/hg19/fa/hg19.fa MIN_AB=10.0 INPUT=12-3455_S6.final.vcf OUTPUT=test.vcf
    But I still got the error:

    [Mon Aug 31 14:09:24 CEST 2015] picard.vcf.filter.FilterVcf INPUT=2-3455_S6.final.vcf OUTPUT=test.vcf MIN_AB=10.0 REFERENCE_SEQUENCE=/lustre1/genomes/hg19/fa/hg19.fa MIN_DP=0 MIN_GQ=0 MAX_FS=1.7976931348623157E308 MIN_QD=0.0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
    [Mon Aug 31 14:09:24 CEST 2015] Executing as smerella@b002 on Linux 2.6.32-279.2.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_45-b18; Picard version: 1.138() JdkDeflater
    [Mon Aug 31 14:09:29 CEST 2015] picard.vcf.filter.FilterVcf done. Elapsed time: 0.08 minutes.
    Runtime.totalMemory()=1138753536
    To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
    Exception in thread "main" java.lang.IllegalArgumentException: A reference dictionary is required for creating Tribble indices on the fly
    at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.build(VariantContextWriterBuilder.java:389)
    at picard.vcf.filter.FilterVcf.doWork(FilterVcf.java:97)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

    Issue · Github
    by Sheila

    Issue Number
    274
    State
    closed
    Last Updated
    Closed By
    vdauwera
  • SheilaSheila Broad InstitutePosts: 4,858 admin

    @merella.stefania
    Hi,

    This seems like a bug, so I just submitted a bug report. Thanks for reporting this.

    I will let you know when a fix is in.

    -Sheila

  • merella.stefaniamerella.stefania ItalyPosts: 28

    Thanks Sheila!!
    Let me know when the bug is solved!

    Stefania

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,736 admin

    I don't think this is a bug. The line

    reference dictionary is required for creating Tribble indices on the fly

    Suggests that the .dict file is missing. See the FAQ on reference file input requirements.

    Geraldine Van der Auwera, PhD

  • merella.stefaniamerella.stefania ItalyPosts: 28

    Thanks Geraldine for the answer.
    In the directory /lustre1/genomes/hg19/fa/ I have the file hg19.dict:

    [smerella@b002 utilities]$ head /lustre1/genomes/hg19/fa/hg19.dict
    @HD VN:1.0 SO:unsorted
    @SQ SN:chr1 LN:249250621 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:1b22b98cdeb4a9304cb5d48026a85128
    @SQ SN:chr2 LN:243199373 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:a0d9851da00400dec1098a9255ac712e
    @SQ SN:chr3 LN:198022430 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:641e4338fa8d52a5b781bd2a2c08d3c3
    @SQ SN:chr4 LN:191154276 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:23dccd106897542ad87d2765d28a19a1
    @SQ SN:chr5 LN:180915260 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:0740173db9ffd264d728f32784845cd7
    @SQ SN:chr6 LN:171115067 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:1d3a93a248d92a729ee764823acbbc6b
    @SQ SN:chr7 LN:159138663 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:618366e953d6aaad97dbe4777c29375e
    @SQ SN:chrX LN:155270560 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:7e0e2e580297b7764e31dbc80c2540dd
    @SQ SN:chr8 LN:146364022 UR:file:/usr/local/scratch/genomes/hg19/fa/hg19.fa M5:96f514a9929e410c6651697bded59aec

    Is it correct?

    Thanks for the support.

  • SheilaSheila Broad InstitutePosts: 4,858 admin

    @merella.stefania
    Hi Stefania,

    I have confirmed this is a bug. You have done things correctly.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,736 admin

    Yep, I commented too soon -- Sheila reproduced the bug on our own files.

    You may be able to work around this by generating an index file for your VCF; I believe the dictionary only needs to be loaded if the VCF does not have an index. But I could be wrong.

    Geraldine Van der Auwera, PhD

  • merella.stefaniamerella.stefania ItalyPosts: 28

    @Sheila
    Hi! Any news about the bug?

    Thanks!!

  • SheilaSheila Broad InstitutePosts: 4,858 admin

    @merella.stefania
    Hi Stefania,

    No, sorry. I think you will have to wait a while for this unfortunately. The developers are swamped with other higher priority issues now.

    -Sheila

  • merella.stefaniamerella.stefania ItalyPosts: 28

    Ok thanks Sheila!

  • SheilaSheila Broad InstitutePosts: 4,858 admin

    @merella.stefania
    Hi Stefania,

    The fix will be in the next Picard release. For now, you can get around this issue by outputting a compressed VCF.

    -Sheila

  • merella.stefaniamerella.stefania ItalyPosts: 28

    @Sheila
    Hi Sheila,
    With compressed VCF you mean a BCF file, correct? Then I have to run the command in this way:
    java -jar picard.jar FilterVcf REFERENCE_SEQUENCE=/lustre1/genomes/hg19/fa/hg19.fa MIN_AB=10.0 INPUT=12-3455_S6.final.vcf OUTPUT=test.bcf

    Thanks for the support!!

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