Post date: Mar 30, 2020 2:48:4 PM
useful funtion to get the full path: readlink -f file.ext
Pando_lowhets_50.vcf is the same file as Pando_50.vcf (maybe I wanted to simplify the names)
I am doing the same with Pando_80
Pando_lowhets_80.vcf becomes Pando_80.vcf
STEP 1 - COMPARE DICTS, find common SNPs between all of the trees (Créer le "common_all_80")
Script: /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/variants/pando_only_variants/scripts/compare_dict.py
Command: compare_dict("common_pando_friends_80.dict", "common_pando_pon_80.dict", "common_SNPs_pando_pon_friends_80.dict"
Output: common_SNPs_pando_pon_friends_80.dict - 507 SNPs in common between all of them
STEP 2 - FILTER VCF FROM DICT
Script: /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/variants/pando_only_variants/scripts/filter_vcf_from_dict.py
Command: filter_vcf_from_dict("common_SNPs_pando_pon_friends_80.dict", "../vcf/filtered2xHiCov_pando_only_variants.vcf", "common_all_80.vcf")
Output: 507 common_all_80.vcf
STEP 3 - COMPARE VCFs
A - STRINGENT FILTER
A-1- compare Pando and friends, keep difference only
Command: compare_vcf("pando_80.vcf", "common_friends_pando_80.vcf", "pando_80_friends_filtered.vcf")
Output: 9981 pando_80_friends_filtered.vcf
A-2- compare pando_80_friends_filtered.vcf and pon, keep difference only
Command: compare_vcf("pando_80_friends_filtered.vcf", "common_pon_pando_80.vcf", "pando_80_stringent_filter.vcf")
Output: 8826 pando_80_stringent_filter.vcf
B - NON STRINGENT FILTER
script: /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/variants/pando_only_variants/scripts/compare_two_vcf.py
command: compare_vcf("pando_80.vcf", "common_all_80.vcf", "pando_80_non_stringent_filter.vcf")
output: 10689 pando_80_non_stringent_filter.vcf
STEP 4 - GET GENOTYPES LIKELIHOODS
Script: /uufs/chpc.utah.edu/common/home/u6028866/data/Pando/variants/pando_only_variants/scripts/convert_score_to_proba.py
Command: revert_score("pando_80_stringent_filter.vcf","20200330_80hets_proba.txt")
Output: 8826 20200330_80hets_proba_stringent_filter.txt
STEP 5 - ANALYSES Download the txt file on my computer to run the analyses