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Thank you Shelia. Just to clarify, for a joint analysis it is recommended that BaseRecalibrator be run separately for each sample to generate sample-specific base recalibration tables. These recalibration are then used by PrintReads to generate m…
Thank you Geraldine. To be clear, each iteration uses a different set of 'known' variants to generate a recalibration table; and the tables are generated independently of one another? In this case, if a groups of recalibration tables yield similar …
On a related note, when bootstrapping the database of SNPs, is it necessary to run the full halpotypeCaller --> BaseRecallibrator --> PrintReads pipeline for each iteration; or can we simply run haplotypeCaller at the beginning of the run, per…
Is it one or more graph files? Is it one of the table files? If you are comparing the results of three different recalibration runs, can you enter more than one file?
What exactly is the "original recalibration file" file?
Thank you Geraldine, this makes things a lot clearer.
Hi ebanks, GATK was run under the default "USE_READS" option for the consensusDeterminationModel. I have attached an updated screen grab of my alignments before they were realigned. Cheers gwilymh
(Quote) How can HaplotypeCaller be insensitive to the initial alignments? Does it perform some sort of realignment around each suspected polymorphism?
Hi Geraldine, I have attached a file with screen grabs of two of my alignments. The alignments are presented as they are after GATK realignment, and as (I think) they should be after manual realignment. The alignments are displayed in the program G…
I am trying to call SNP genotypes in a number of different individuals, i.e. trying to genotype individuals for a list of known SNPs.