I have several BAM files. Each one of them corresponding to a sample.
According to Germline short variant discovery (SNPs + Indels) Best Practices https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels- the way to obtain a single VCF file with all the variants for a samples cohort would be (1) create a gVCF for each BAM file with HaplotypeCaller in gVCF mode and then (2) pass all of them to GenotypeGVCFs.
However, it is also possible to pass HaplotypeCaller several BAM files as inputs. So, if I give HaplotypeCaller my sample BAM files as inputs, will I obtain the same VCF as in the best practices method I have described above?
Sorry if I miss something important, I am pretty new in using GATK.
Thanks in advance for your time.
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