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GATK4 haplotypecaller doesn't genotype multiple bams

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In GATK3, using multiple bams in the -I parameter would print multiple columns of genotypes. This doesnt seem to happen with GATK4. Here is the command

    gatk --java-options "-Xmx60G" HaplotypeCaller \
    -I $BAM1 \
    -I $BAM2 \
     --genotyping-mode DISCOVERY \
    -R $ref \
    -D $dbsnp \
    -O $out_directory$fname.el.snps.vcf

Here is the output

##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller  --dbsnp /home/exacloud/tempwork/SpellmanLab/heskett/DBSNP_150_uw.vcf --genotyping-mode DISCOVERY --output 4e700.sorted.de-duplicated.recalibrated.el.snps.vcf --input 4e700.sorted.de-duplicated.recalibrate
d.bam --input 4l700.sorted.de-duplicated.recalibrated.bam --reference /home/exacloud/lustre1/SpellmanLab/heskett/refs/myron_refs/human_g1k_v37.fasta


#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  1
1       12783   rs62635284      G       A       251.77  .       AC=2;AF=1.00;AN=2;DB;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=25.24;QD=25.18;SOR=4.804     GT:AD:DP:GQ:PL  1/1:0,10:10:30:280,30,0
1       13116   rs62635286      T       G       710.77  .       AC=2;AF=1.00;AN=2;DB;DP=17;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=28.05;QD=25.36;SOR=0.804     GT:AD:DP:GQ:PL  1/1:0,17:17:51:739,51,0
1       13118   rs62028691      A       G       710.77  .       AC=2;AF=1.00;AN=2;DB;DP=15;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=26.73;QD=28.73;SOR=0.818     GT:AD:DP:GQ:PL  1/1:0,15:15:51:739,51,0

is this feature not implemented yet? or did the command line call change?

Thanks!


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