Update column names for gnomad v4 update

[anjalijain22]

• Updated column names to reflect new columns in gnomad v4 update such as Gnomad_fafmax_faf95_max and Gnomad_af_grpmax
• Use this cre branch in conjunction with this crg2 branch gnomad V4 update crg2#231

[Madelinehazel]

Looks great! Do you mind moving the Gnomad_male_ac column next to Gnomad_hom ? I know this is just inherited from the hg19 pipeline but we might as well move it (e.g. I changed it for crg2-pacbio).

I'm wondering if we should now be filtering on Gnomad_fafmax_faf95_max instead of Gnomad_af_grpmax. My understanding is that Gnomad_fafmax_faf95_max corresponds to the GroupMax filtering allele frequency (FAF), which excludes bottlenecked genetic ancestry groups. The FAF is described here.

[anjalijain22]

Changes:

• Rearranged the gnomAD columns to be together in the report
• Filtering by gnomAD_fafmax_faf95_max column
• Added new constraint scores from gnomAD v4.1
• Updated scripts to be used by Slurm Scheduler

Issues to be addressed before merging:
gnomAD_fafmax_faf95_max is missing for a lot of variants. It seems like it should be 0 for these variants according to this post but this requires more clarification before hardcoding it into the pipeline: https://discuss.gnomad.broadinstitute.org/t/groupmax-values-missing-for-a-lot-of-variants/250