I am currently looking at the GATK 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#6.2) and I noticed that in workflow 3, there is an input file called altalt.sam but I do not know where this file came from. There is no prior reference to this file in the tutorial so I am wondering if altalt.sam is the same as 8017bwamem.sam from bwa mem in the tutorial? If so, then the output from this command (k8 bwa-postalt.js) would come directly before steps 4.1-4.7?
Thank you in advance!
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