We would like to add LINSIGHT into the annotation pipeline for the hg38 version of crg2 to predict the fitness consequences of non-coding mutations.
GRCh38 LINSIGHT scores can be downloaded from this link.
You will need to:
- Download the BED file of scores to /hpf/largeprojects/ccmbio/nhanafi/c4r/downloads/databases/.
- Examine the fields in the file. The score is the fourth column.
- Checkout the hg38 branch of crg2: inside your local crg2 directory, type
git checkout crg2-hg38
- Modify the vcfanno config to add the LINSIGHT 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
We would like to add LINSIGHT into the annotation pipeline for the hg38 version of crg2 to predict the fitness consequences of non-coding mutations.
GRCh38 LINSIGHT scores can be downloaded from this link.
You will need to:
git checkout crg2-hg38