hi, i am trying to understand how the various re-alignment or alignment adjustment tools vary.
from samtools mpileup docs
but in the samtools calmd help, it lists for option -r:
is the disctintion here that tools like SRMA consider the other alignments/reads whereas samtools does a realignment but only considers the reference and the current read?
how does this relate to GATK's Base quality score recalibration?
thanks in advance
from samtools mpileup docs
One way to avoid such an artifact is to do multi-sequence realignment ... SAMtools seeks another solution
-r read-independent local realignment
is the disctintion here that tools like SRMA consider the other alignments/reads whereas samtools does a realignment but only considers the reference and the current read?
how does this relate to GATK's Base quality score recalibration?
thanks in advance
Comment