Incorporate FATHMM-XF into annotation pipeline

[Madelinehazel]

We would like to add FATHMM-XF into the annotation pipeline for the hg38 version of crg2 to predict the fitness consequences of non-coding mutations.

GRCh38 ncER scores can be found at /hpf/largeprojects/ccmbio/pxu/DATABASE/GREEN-DB/GRCh38_FATHMM-XF_NC.tsv.gz.

You will need to:

Copy the BED file of scores to /hpf/largeprojects/ccmbio/nhanafi/c4r/downloads/databases/.
Examine the fields in the file. The score is the fifth column.
Checkout the hg38 branch of crg2: inside your local crg2 directory, type git checkout crg2-hg38
Modify the vcfanno config to add the FATHMM-XF score using vcfanno (see other score annotations, e.g. CADD for an example of how to do this)
Setup a test run of the pipeline using the NA12878 BAM specified in the default units.tsv:
Set the target in dnaseq_slurm_hpf.sh to annotated/coding/vcfanno/NA12878.coding.vep.vcfanno.vcf
Submit the pipeline job