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Scripts for analyses and figures for SNP STR Imputation manuscript
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L1O_Analysis
beagle_phase_strs
filter_hipstr_calls
hipstr_str_calling
notebooks
shapeit_phasing
ssc-pca
utils
README.md

README.md

Scripts and analyses for SNP-STR imputation manuscript

beagle_phase_strs

Scripts to phase STR loci on XSEDE cluster computing environment. In the the genfiles_100.sh file, edit the chromosome and input VCF files. Execute the file. Then run the generated pilot.sh file to phase 100 STRs per compute job.

filter_hipstr_calls

Scripts to filter HipSTR calls on the XSEDE cluster computing environment.

hipstr_str_calling

Scripts to call STRs using HipSTR on Amazon AWS.

./launch_aws.sh "aws_access_key" "aws_secret_key" "chrosome" "[parts]" "volume size" "batch_size" "keyname"

L1O_Analysis

Scripts to perform leave-one-out trials on XSEDE cluster computing environment. Usage:

sbatch -p shared \
-A ddp268 \
-t 0-12:00 \
--job-name=chr21loo \
--mem=5G \
-c 1 \
--get-user-env \
./runme.sh hipstr.calls.chr21.vcf.gz snps.chr21.vcf.gz chr21.snp.str.vcf.gz 21

shapeit_phasing

Scripts to phase SNP haplotypes using SHAPEIT

./phase.sh -v unphased.snps.vcf.gz \
-f pedigree.txt \
-s /path/to/shapeit \
-b /path/to/bcftools \
-p /path/to/plink \
-m directory_to_genetic_maps \
-q createFam.py

ssc-pca

Scripts to perform PCA using 1000 genomes reference panel Input: snps.vcf.gz, 1000genomes.samples.txt Usage:

./script.sh -s ssc.vcf.gz -r ref.samples -c 21
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