⛸️Further

There are more functions but would make the docker image huge! So we list the guidance here, you can install them as you need.

AnnotSV for SV Annotation

See:https://github.com/lgmgeo/AnnotSV/blob/master/share/doc/AnnotSV/quickstart.md

Annovar for SNV Annotation

A easy way to install all-in-one Annovar is through this website:

See:https://github.com/geniusphil/2019GenomicsEpidemiologyWorkshop

Contact us:

Honghyuan Chu: [e-mail]

Huaxia Luo: [e-mail]

Renqiuguo Li: [e-mail]

To Get High Precision Recall Set Using SURVIVOR

#!/bin/bash
source ~/.bashrc
#cd <summer_outdir>
######################################################
#           Merging high precision SVs               #
######################################################
#Filter QUAL
bcftools view -f PASS /opt/outdir/cutesvout.vcf > cutesv_pass.vcf
bcftools view -f PASS /opt/outdir/sample_sniffles2.vcf > sniffles2_pass.vcf
bcftools view -f PASS /opt/outdir/svimoutput/signatures/all.vcf > svim_pass.vcf
#Filter GT
bcftools view -e 'GT="0/0" || GT="./." || GT=".|."' sniffles2_pass.vcf -o sniffles2_pass_gt.vcf 
bcftools view -e 'GT="0/0" || GT="./." || GT=".|."' svim_pass.vcf -o svim_pass_gt.vcf 
bcftools view -e 'GT="0/0" || GT="./." || GT=".|."' cutesv_pass.vcf -o cutesv_pass_gt.vcf
#Merge file names
ls cutesv_pass_gt.vcf svim_pass_gt.vcf sniffles2_pass_gt.vcf > sample_files
#SURVIVOR
SURVIVOR merge sample_files 1000 2 1 0 0 50 high_precision_merge.vcf
# rm *_pass.vcf *_pass_gt.vcf sample_files
####in case to remove intermediate files

To Download List of STRs Across Whole Genome: https://webstr.ucsd.edu/downloads