Map reads with alternate contigs

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Linda Do

• January 30, 2021 22:22

Hi, I am new to GATK. In the tutorial for (How to) Map reads to a reference with alternate contigs like GRCH38 (https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38#1), after indexing the reference, it starts with 2 fastq files (forward and reverse). 

I have bam files that I have reverted to ubam files. Would I still be able to use this tutorial without having the fastq files?

For example, instead of using the command "bwa mem referencepath fastq1path fastq2path > bampath" as in the tutorial,

can I use the single fastq file from SamToFastq (convert my bam to a fastq) for "bwa mem referencepath SamToFastqOutput > bampath"?

I am unsure if this would result in different analysis as I do not know for sure that the downstream GATK tutorial tools would work the same when the starting file is different.

If this does not work, is there a way to use this tutorial by reverting the bam files to the necessary paired fastq files?

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Thank you in advance!

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  Genevieve Brandt (she/her)

  • February 02, 2021 19:55

  Hi Linda Do, it looks like you have come up with a great solution! I believe it should work. After doing that step, follow along with the directions checking if the BAM was aligned with alt-handling to make sure that your solution worked.

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  Linda Do

  • April 05, 2021 05:22

  Thank you for your answer!

  I will try it!

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