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UnifiedGenotyper gives empty vcf file on exampleBAM.bam

w2033804w2033804 PhoenixPosts: 3Member
edited October 2013 in Ask the GATK team

Hi, I‘m trying UnifiedGenotyper on the exampleBAM.bam in source/ , but it generated empty vcf files. Here's my command:

java -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R exampleFASTA.fasta -I exampleBAM.bam -o test.vcf -stand_emit_conf 10.0

Gives me this output:

INFO 00:02:40,348 HelpFormatter - --------------------------------------------------------------------------------

INFO 00:02:40,354 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-4-g6f46d11, Compiled 2013/10/10 17:27:51

INFO 00:02:40,354 HelpFormatter - Copyright (c) 2010 The Broad Institute

INFO 00:02:40,355 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk

INFO 00:02:40,361 HelpFormatter - Program Args: -T UnifiedGenotyper -R exampleFASTA.fasta -I exampleBAM.bam --o test.vcf -stand_emit_conf 10.0

INFO 00:02:40,362 HelpFormatter - Date/Time: 2013/10/26 00:02:40

INFO 00:02:40,362 HelpFormatter - --------------------------------------------------------------------------------

INFO 00:02:40,362 HelpFormatter - --------------------------------------------------------------------------------

INFO 00:02:42,599 GenomeAnalysisEngine - Strictness is SILENT

INFO 00:02:43,102 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250

INFO 00:02:43,115 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

INFO 00:02:43,162 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05

INFO 00:02:43,559 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files

INFO 00:02:43,598 GenomeAnalysisEngine - Done preparing for traversal

INFO 00:02:43,598 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]

INFO 00:02:43,598 ProgressMeter - Location processed.sites runtime per.1M.sites completed total.runtime remaining

INFO 00:02:53,993 ProgressMeter - done 1.00e+05 10.0 s 103.0 s 99.9% 10.0 s 0.0 s

INFO 00:02:53,994 ProgressMeter - Total runtime 10.40 secs, 0.17 min, 0.00 hours

INFO 00:02:53,994 MicroScheduler - 0 reads were filtered out during the traversal out of approximately 33 total reads (0.00%)

INFO 00:02:53,995 MicroScheduler - -> 0 reads (0.00% of total) failing BadMateFilter

INFO 00:02:53,995 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter

INFO 00:02:53,996 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter

INFO 00:02:53,996 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter

INFO 00:02:53,996 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter

INFO 00:02:53,997 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter

INFO 00:02:53,997 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter

INFO 00:03:06,010 GATKRunReport - Uploaded run statistics report to AWS S3

And the test.vcf is empty with only titles. I have attached this file.

Does anyone see where I made a mistake? Is there another setting which I have to set for finding a SNP in the sample data? Thanks.

txt
txt
test.vcf.txt
6K
Post edited by w2033804 on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,756Administrator, GATK Dev admin

    Hi there,

    The exampleBAM does not have enough data to actually call SNPs on it. It's only provided to quickly test very basic commands when you start out with GATK. For test datasets that you can actually perform the Best Practices steps on, including variant calling with the UG, please see the resource bundle we provide on our FTP server.

    Geraldine Van der Auwera, PhD

  • w2033804w2033804 PhoenixPosts: 3Member
    edited October 2013

    Thanks for your help. I accessed you FTP server. The files in your /bundle/2.5/exampleFASTA/ directory are exactly same as I used. Could you give me any clue that which files I should use to practices UG? Or a README file about the explanation of your bundle? Thanks.

    Post edited by w2033804 on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,756Administrator, GATK Dev admin

    Please see the resource bundle FAQ here: http://www.broadinstitute.org/gatk/guide/article?id=1213

    Geraldine Van der Auwera, PhD

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