HaplotypeCaller using one sample split in two bam files

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elena vigorito

• June 28, 2022 09:16

I have a sample that has been split and ran in two different machines. For that sample I have reads with two different read groups and in 2 pairs of fastq files.  Would be okay to align them separately so I will obtain 2 different bam files, each of the bam files will have the appropriate read group. Would be then possible to pass those 2 bam files to the base quality recalibration tool and then to the haplotypecaller? Otherwise, could you please suggest how to deal with this?

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  Anthony DiCi

  • June 28, 2022 16:29

  Thank you for your post, elena vigorito ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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  Anthony DiCi

  • September 22, 2022 18:47

  Hi elena vigorito,

  Thank you for writing to the GATK forum! I hope that we can help you sort this out.

  In this case, you can use the MergeSamFiles (Picard) tool. This tool will allow you to merge your BAM files from different read groups into a single file. You’ll want to combine these before inputting them into HaplotypeCaller. Please find an example command below.

  java -jar picard.jar MergeSamFiles \
       I=input_1.bam \
       I=input_2.bam \
       O=output_merged_files.bam

  I hope this helps! Please let me know if you find success with this. If you have any other questions, please do not hesitate to reach out.

  Best,
  Anthony

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  Anthony DiCi

  • September 29, 2022 15:01

  Hi elena vigorito,

  We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll create a follow-up ticket to pick up where we left off.

  Thank you again for contributing to our GATK forum!

  Best,

  Anthony

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