Hi everybody,
I am new in NGS analysis and hope not to ask something already solved (or discussed), in that case please only refer me to the right discussion.
I am writing an analysis pipeline, based on gatk, to analyse exome data.
My question is: which step of the gatk is better to do on multiple samples?
I figured out the following pipeline up to the UnifiedGenotyper:
dedupplig (single sample) ->
RealignTargetCreator (multiple) ->
IndelRealigner (single) ->
BaseRecalibrator (multiple) ->
UnifiedGenotyper (multiple)
Is this correct?
Thank you
I am new in NGS analysis and hope not to ask something already solved (or discussed), in that case please only refer me to the right discussion.
I am writing an analysis pipeline, based on gatk, to analyse exome data.
My question is: which step of the gatk is better to do on multiple samples?
I figured out the following pipeline up to the UnifiedGenotyper:
dedupplig (single sample) ->
RealignTargetCreator (multiple) ->
IndelRealigner (single) ->
BaseRecalibrator (multiple) ->
UnifiedGenotyper (multiple)
Is this correct?
Thank you