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Thanks for the reply! I will now manually remove filtered sites for downstream tools to be on the safe side.
I have a question about the population germline variant resource used in Mutect2 and in making the Panel of Normals. My main question is this: Can I use a bootstrapped-knownSites.vcf that I generated with HaplotypeCaller in the BQSR process as the …
I found on another thread that the -BQSR flag no longer works for on-the-fly recalibration in GATK4. Can you please update the documentation to reflect that? Specifically this article as it still says to use BaseRecalibrator + BQSR instead of ApplyB…
I’m trying to run Step 2 where I do a second pass to analyze covariation, but I keep getting an error whenever it tries to read the -BQSR <recal.table> flag. This is my code for the command: gatk BaseRecalibrator \ -R="$REF_GENOME_FASTA&…
Thanks @Sheila , one more question: I am calling mutations between 5 tumor-normal pairs of the same strain of mouse from the same sequencing run. Can I use all 5 of the normal.bams for bootstrapping the raw.vcf>>>knownSites.vcf>>>…
@Sheila , If I am bootstrapping a knownSites.vcf to use in recalibration of both a tumor and normal BAM file, should I only use the normal BAM when making the bootstrapped knownSites.vcf? Or should I plug both the tumor and normal BAM in when runnin…
Of course I would find in  that the very first example uses two --known-sites=SNP.vcf --known-sites=indel.vcf options... Question answered, I guess.
(Quote) I needed it spelled out for me like this. Thank you. The GATK preprocessing instructions are very unclear and made it sound like I needed to align the uBAM with BWA...