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Bug? (making Pileup file)

airyspaceairyspace Posts: 2Member
edited September 2012 in Ask the GATK team

Dear GATK team

I tried following commands to validate SNP calling (Comparing with SNP Array data)

$ java -jar /usr/local/GenomeAnalysisTK-2.1-5-gf3daab0/GenomeAnalysisTK.jar -T Pileup --showVerbose -R ./human_g1k_v37.fasta -I Sample.final.bam -o Sample.final.pileup
$ java -Xmx2g -jar /usr/local/GenomeAnalysisTK-2.1-5-gf3daab0/GenomeAnalysisTK.jar -R ./human_g1k_v37.fasta -T VariantsToVCF -o Sample.pileup.vcf --variant:SAMPILEUP Sample.final.pileup --dbsnp /home/database/broadinstitute/1.2/b37/dbsnp_132.b37.vcf

then, I got error message like this

"ERROR MESSAGE: the SAM pileup line didn't have the expected number of tokens (expected = 10, saw = 1 on line = 1 14369 C CCCCCCCCCC GGGCC#CIHG"

$ head Sample.final.pileup
1 14369 C CCCCCCCCCC GGGCC#CIHG

Do you have any idea??

Post edited by Geraldine_VdAuwera on
Tagged:

Best Answers

  • Mark_DePristoMark_DePristo Posts: 153Administrator, Dev admin
    Answer ✓

    These are just the wrong commands for what you want to do. Look at UnifiedGenotyper. The Pileup format is really for debugging, more than anything.

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • Mark_DePristoMark_DePristo Posts: 153Administrator, Dev admin
    Answer ✓

    You can use VariantEval for this. Call SNPs with UnifiedGenotyper and then use VariantEval. Docs are all in the Guide section for both tools

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

Answers

  • Mark_DePristoMark_DePristo Posts: 153Administrator, Dev admin
    Answer ✓

    These are just the wrong commands for what you want to do. Look at UnifiedGenotyper. The Pileup format is really for debugging, more than anything.

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

  • airyspaceairyspace Posts: 2Member

    Dear Mark.

    Thank you for your comment,
    Then, could you recommend for me what to do if I want to compare the accuracy using SNP array data ?
    I think it would be easy when UnifiedGenotyper calls SNP which is on SNP array.(get dbSNPID which are detected by GATK and check the array data).
    I want to check all sites on the array.

    Sorry, I wish I could write correct English..

  • Mark_DePristoMark_DePristo Posts: 153Administrator, Dev admin
    Answer ✓

    You can use VariantEval for this. Call SNPs with UnifiedGenotyper and then use VariantEval. Docs are all in the Guide section for both tools

    --
    Mark A. DePristo, Ph.D.
    Co-Director, Medical and Population Genetics
    Broad Institute of MIT and Harvard

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