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oh, and even more important question on the same subject: when I have multiple bam files (multiple read groups due to multiple lanes) for the same sample - how I proceed it for the Calling variants (software.broadinstitute.org/gatk/documentation/art…
Thank you @bhanuGandham ! That video was useful. (What I didn't realize was the concept of the blocks in fact)
Hello, if possible could you please explain how those "potential" (non-variant) sites are detected when we build GVCF? For example, I run HaplotypeCaller for each sample with the following arguments: -I split.bam -O out.g.vcf -R GRCm38.fa …
can this workflow be adapted for mouse RNA-seq data?