Runs through output of FG vs EXOME data and it procudes summaries of correct/incorrect ID mappings
Usage:
bash kinship.sh ./mapping_test/ mapping.kin
Check for paths to kinship data in the script.
Produces a file that can be passed to plink --update-ids in order to update the exome sample ids
Usage:
python3 ~/Dropbox/Projects/misc/exome/assign_id.py /mnt/disks/data/exome/kinship/full_exome/ /mnt/disks/data/exome/plink/exome_merged.fam
First one needs to run exome_annotate.wdl to get a decent subet after filtering for DP/GQ and annotating to CHROM_POS_REF_ALT
Then one needs to convert to plink to shared FG variants and run king to get a kin and kin0 file. One needs to reminds also to convert the plink files to --maj-ref with plink1.
The one can run assign_ids.wdl to assign the mapping from/to exome/fg IDs.
After that one can run 'exome_convert.wdl` to build the vcf/plink/bgen files with the new sample ids
exome_ld.wdl is the wdl where plink FG data is subset to exome samples and exome data is subset to only non FG snps, so that they can be merged and ld run.