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Revision 2e105bf050fd2acb9f1e0d1833566c0b1ca5b41f authored by Stephanie Yan on 23 August 2021, 15:32:48 UTC, committed by Stephanie Yan on 23 August 2021, 15:32:48 UTC 
include moderate LD threshold
1 parent b19a9ee
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calculate_afs.sh 
#!/bin/bash

### Calculates allele frequency of SVs in each population using PLINK.

############################################################################

### DATA

# VCF output from Paragraph; no full SV sequences
INPUT_VCF=eichlerSVs_1KGP_pgGTs_noseq.vcf.gz

# file specifying groups (i.e. populations) to calculate AF in
WITHIN_FILE=1KGP_within.txt

############################################################################


plink --vcf $INPUT_VCF \
	--within $WITHIN_FILE \
	--freq gz \
	--keep-allele-order \
	--out eichlerSVs_af_allpops_unfolded
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