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  • GATK : Drop in number of confidently called bases

    We called the SNPs using GATK v1.0.5506 before and decided to recall using the recent version v1.2-4; however, we found a dramatical decrease in number of confidently called bases from ~90 to ~20%.

    Can anyone suggest what's the problem?

    Here is the old command and summary (taking a small region as an example),

    --------------------------------------------------------------------------------------
    java -Xmx4g -jar GenomeAnalysisTK-1.2-4-gd9ea764/GenomeAnalysisTK.jar \
    -I recalibrated.bam \
    -T UnifiedGenotyper \
    -l INFO \
    -R human_g1k_v37.fa \
    --dbsnp dbsnp_132.b37.vcf \
    -o test.raw.SNP.vcf \
    -metrics test.raw.SNP.variants \
    -glm SNP \
    -stand_call_conf 50 \
    -stand_emit_conf 10 \
    -dcov 500 \
    -nt 1 \
    -L 11:76260000-76270000 \
    -S LENIENT

    ================================
    Visited bases 10001
    Callable bases 9992
    Confidently called bases 152
    % callable bases of all loci 99.910
    % confidently called bases of all loci 1.520
    % confidently called bases of callable loci 1.521
    Actual calls made 5
    --------------------------------------------------------------------------------------
    And the new command
    java -Xmx4g -jar GenomeAnalysisTK-1.0.5506/GenomeAnalysisTK.jar \
    -I recalibrated.bam \
    -T UnifiedGenotyper \
    -l INFO \
    -R human_g1k_v37.fa
    -B:dbsnp,vcf dbsnp_132.b37.vcf \
    -o test.oldUG.raw.SNP.vcf \
    -metrics test.oldUG.variants \
    -glm SNP \
    -stand_call_conf 50 \
    -stand_emit_conf 10 \
    -dcov 500 \
    -nt 1 \
    -L 11:76260000-76270000 \
    -S LENIENT

    ==================================
    Visited bases 10001
    Callable bases 9990
    Confidently called bases 9988
    % callable bases of all loci 99.890
    % confidently called bases of all loci 99.870
    % confidently called bases of callable loci 99.980
    Actual calls made 5

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