Is it possible to pass multiple bams to GATK4 HaplotypeCaller?

srw6vsrw6v United StatesMember

Because of a variety of preprocessing steps that I have to perform on my input bam I have split it by chromosome to make this process faster. Joining these bams together before calling SNVs with HaplotypeCaller is a very time consuming step so it would be most convenient to just pass all the bams at once without the join. Is it possible to pass multiple bams to HaplotypeCaller? I have tried a variety of ways such as

gatk-launch HaplotypeCaller -R hg19-1.2.0/fasta/genome.fa -I example.20.bam -I example.21.bam -O out.vcf

and the Mutect2 way

gatk-launch HaplotypeCaller -R hg19-1.2.0/fasta/genome.fa -I:20 example.20.bam -I:21 example.21.bam -O out.vcf

Is this even possible?

Thanks very much,

Stephen

Best Answer

  • srw6vsrw6v United States
    Accepted Answer

    SOLVED

    Sorry for the question. I figured it out. I did not have the sample information in the bam header.

    gatk-launch HaplotypeCaller -R hg19-1.2.0/fasta/genome.fa -I example.20.bam -I example.21.bam -O out.vcf
    

    works

Answers

  • srw6vsrw6v United StatesMember
    Accepted Answer

    SOLVED

    Sorry for the question. I figured it out. I did not have the sample information in the bam header.

    gatk-launch HaplotypeCaller -R hg19-1.2.0/fasta/genome.fa -I example.20.bam -I example.21.bam -O out.vcf
    

    works

  • heskettheskett Portland, Oregon. USAMember

    can you elaborate on this?

    It seems like the behavior is different from GATK3 haplotypecaller

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @heskett
    Hi,

    You can pass in multiple BAM files when running in normal mode. However, when running in GVCF mode, you cannot pass in multiple BAM files.

    -Sheila

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