Feature Request: Making BQSR optional

[Alfredo-Enrique]

Feature Request: We may benefit from making BQSR optional.

In the past, we've encountered instances where some bam files only have recalibrated quality scores and not original quality scores. In those cases, it may be beneficial to have an option in call-gSNP to skip base quality score recalibration. Otherwise, within the current worklfow of bam2fastq -> align-DNA -> call-gSNP we will be applying BQSR twice.

Again this only applies in only the few cases where there are no original quality score. You see this sometimes in sometimes in TCGA bams.

Low priority, but adding it here just in case someone is wondering.

[tyamaguchi-ucla]

@yashpatel6 Consider moving this issue to https://github.com/uclahs-cds/pipeline-recalibrate-BAM

[yashpatel6]

To add on, this parameterization can be extended to INDEL Realignment as well