Post date: May 01, 2020 5:43:37 PM
Try with more stringent filters to see if there is a spatial structure in the data.
Step 3b) create bool based on filter: less than 20% and less than 5% hets per SNPs
Step 3c) filter vcf based on bool
7186 pando_only_variants_20_hets.vcf
3527 pando_only_variants_05_hets.vcf
Step 4) create dict
7186 pando_only_variants_20_hets.dict
3527 pando_only_variants_05_hets.dict
Step 5) Compare dictionaries and separate similarities from differences (filtering for common SNPs)
717 intersection_SNPs_pando_friends_20.dict
1104 intersection_SNPs_pando_pon_20.dict
314 intersection_all_20.dict
305 intersection_SNPs_pando_friends_05.dict
539 intersection_SNPs_pando_pon_05.dict
125 intersection_all_05.dict
Step 6) filter vcf file from dict, keep intersection.
Step 7) filter vcf from vcf, keep difference.
314 intersection_SNPs_all_20.vcf
717 intersection_SNPs_pando_friends_20.vcf
1104 intersection_SNPs_pando_pon_20.vcf
125 intersection_SNPs_all_05.vcf
305 intersection_SNPs_pando_friends_05.vcf
539 intersection_SNPs_pando_pon_05.vcf
6872 difference_SNPs_all_20.vcf
6469 difference_SNPs_pando_friends_20.vcf
6082 difference_SNPs_pando_pon_20.vcf
5679 difference_SNPs_stringent_filter_20.vcf
3402 difference_SNPs_all_05.vcf
3222 difference_SNPs_pando_friends_05.vcf
2988 difference_SNPs_pando_pon_05.vcf
2808 difference_SNPs_stringent_filter_05.vcf
Step 8) Extract proba hets.
6872 difference_SNPs_all_20.txt
6469 difference_SNPs_pando_friends_20.txt
6082 difference_SNPs_pando_pon_20.txt
5679 difference_SNPs_stringent_filter_20.txt
717 intersection_SNPs_pando_friends_20.txt
1104 intersection_SNPs_pando_pon_20.txt
3402 difference_SNPs_all_05.txt
3222 difference_SNPs_pando_friends_05.txt
2988 difference_SNPs_pando_pon_05.txt
2808 difference_SNPs_stringent_filter_05.txt
305 intersection_SNPs_pando_friends_05.txt
539 intersection_SNPs_pando_pon_05.txt