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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