So this is why we keep electronc notebooks, I went back to my old Geoduck stuff, grabbed the relatedness matrix stuff, and cut and paste.

setwd("~/Documents/C-virginica-BSSeq/MethylExtract/VCFs/")
vcf.filenames<- list.files(path = ".", pattern = ".vcf")
## Goes through and bgzips and tabixs each file, a requirement of vcf-merge
for(i in 1:length(vcf.filenames))   {
  
  system(paste0("bgzip -c ", vcf.filenames[i], " > ", substr(vcf.filenames[i],1 , 22), ".gz"))
  system(paste0("tabix ", substr(vcf.filenames[i],1 , 22), ".gz"))
  
}
list.files(path = ".", pattern = "*.*")
 [1] "2112_lane1_ACAGTG_SNVs.gz"     "2112_lane1_ACAGTG_SNVs.gz.tbi" "2112_lane1_ACAGTG_SNVs.vcf"   
 [4] "2112_lane1_ATCACG_SNVs.gz"     "2112_lane1_ATCACG_SNVs.gz.tbi" "2112_lane1_ATCACG_SNVs.vcf"   
 [7] "2112_lane1_CAGATC_SNVs.gz"     "2112_lane1_CAGATC_SNVs.gz.tbi" "2112_lane1_CAGATC_SNVs.vcf"   
[10] "2112_lane1_GCCAAT_SNVs.gz"     "2112_lane1_GCCAAT_SNVs.gz.tbi" "2112_lane1_GCCAAT_SNVs.vcf"   
[13] "2112_lane1_TGACCA_SNVs.gz"     "2112_lane1_TGACCA_SNVs.gz.tbi" "2112_lane1_TGACCA_SNVs.vcf"   
[16] "2112_lane1_TTAGGC_SNVs.gz"     "2112_lane1_TTAGGC_SNVs.gz.tbi" "2112_lane1_TTAGGC_SNVs.vcf"   
## performes the actual merge on all avaialble bgzipped files. It would be wise to only have VCF files in this directory, so strange things don't happen.
setwd("~/Documents/C-virginica-BSSeq/MethylExtract/VCFs/")
system("vcf-merge *.gz > merged.vcf")

gzip: stdout: Broken pipe
Using column name 'NA0001' for 2112_lane1_ACAGTG_SNVs.gz:NA0001

gzip: stdout: Broken pipe
Using column name '2112_lane1_ATCACG_SNVs_NA0001' for 2112_lane1_ATCACG_SNVs.gz:NA0001

gzip: stdout: Broken pipe
Using column name '2112_lane1_CAGATC_SNVs_NA0001' for 2112_lane1_CAGATC_SNVs.gz:NA0001

gzip: stdout: Broken pipe
Using column name '2112_lane1_GCCAAT_SNVs_NA0001' for 2112_lane1_GCCAAT_SNVs.gz:NA0001

gzip: stdout: Broken pipe
Using column name '2112_lane1_TGACCA_SNVs_NA0001' for 2112_lane1_TGACCA_SNVs.gz:NA0001

gzip: stdout: Broken pipe
Using column name '2112_lane1_TTAGGC_SNVs_NA0001' for 2112_lane1_TTAGGC_SNVs.gz:NA0001
system("vcftools --relatedness --vcf merged.vcf --out relatedness")

VCFtools - UNKNOWN
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf merged.vcf
    --out relatedness
    --relatedness

After filtering, kept 6 out of 6 Individuals
Outputting Individual Relatedness
    Relatedness: Only using fully diploid sites.
    Relatedness: Only using biallelic sites.
After filtering, kept 307273 out of a possible 307273 Sites
Run Time = 2.00 seconds
system("head relatedness.relatedness")
INDV1   INDV2   RELATEDNESS_AJK
NA0001  NA0001  0.909934
NA0001  2112_lane1_ATCACG_SNVs_NA0001   -0.104487
NA0001  2112_lane1_CAGATC_SNVs_NA0001   -0.0215528
NA0001  2112_lane1_GCCAAT_SNVs_NA0001   -0.276806
NA0001  2112_lane1_TGACCA_SNVs_NA0001   -0.120841
NA0001  2112_lane1_TTAGGC_SNVs_NA0001   -0.103631
2112_lane1_ATCACG_SNVs_NA0001   2112_lane1_ATCACG_SNVs_NA0001   0.893281
2112_lane1_ATCACG_SNVs_NA0001   2112_lane1_CAGATC_SNVs_NA0001   -0.0845831
2112_lane1_ATCACG_SNVs_NA0001   2112_lane1_GCCAAT_SNVs_NA0001   -0.339836

That looks like my relatedness matrix. Now off to Excel to make the complete matrix for Macau.

LS0tCnRpdGxlOiAiQy4gdmlyZ2luaWNhIHJlbGF0ZWRuZXNzIG1hdHJpeCIKb3V0cHV0OiBodG1sX25vdGVib29rCi0tLQoKU28gdGhpcyBpcyB3aHkgd2Uga2VlcCBlbGVjdHJvbmMgbm90ZWJvb2tzLCBJIHdlbnQgYmFjayB0byBteSBvbGQgR2VvZHVjayBzdHVmZiwgZ3JhYmJlZCB0aGUgcmVsYXRlZG5lc3MgbWF0cml4IHN0dWZmLCBhbmQgY3V0IGFuZCBwYXN0ZS4gCgpgYGB7cn0KCnNldHdkKCJ+L0RvY3VtZW50cy9DLXZpcmdpbmljYS1CU1NlcS9NZXRoeWxFeHRyYWN0L1ZDRnMvIikKCnZjZi5maWxlbmFtZXM8LSBsaXN0LmZpbGVzKHBhdGggPSAiLiIsIHBhdHRlcm4gPSAiLnZjZiIpCiMjIEdvZXMgdGhyb3VnaCBhbmQgYmd6aXBzIGFuZCB0YWJpeHMgZWFjaCBmaWxlLCBhIHJlcXVpcmVtZW50IG9mIHZjZi1tZXJnZQpmb3IoaSBpbiAxOmxlbmd0aCh2Y2YuZmlsZW5hbWVzKSkgICB7CiAgCiAgc3lzdGVtKHBhc3RlMCgiYmd6aXAgLWMgIiwgdmNmLmZpbGVuYW1lc1tpXSwgIiA+ICIsIHN1YnN0cih2Y2YuZmlsZW5hbWVzW2ldLDEgLCAyMiksICIuZ3oiKSkKICBzeXN0ZW0ocGFzdGUwKCJ0YWJpeCAiLCBzdWJzdHIodmNmLmZpbGVuYW1lc1tpXSwxICwgMjIpLCAiLmd6IikpCiAgCn0KCmxpc3QuZmlsZXMocGF0aCA9ICIuIiwgcGF0dGVybiA9ICIqLioiKQpgYGAKCmBgYHtyfQojIyBwZXJmb3JtZXMgdGhlIGFjdHVhbCBtZXJnZSBvbiBhbGwgYXZhaWFsYmxlIGJnemlwcGVkIGZpbGVzLiBJdCB3b3VsZCBiZSB3aXNlIHRvIG9ubHkgaGF2ZSBWQ0YgZmlsZXMgaW4gdGhpcyBkaXJlY3RvcnksIHNvIHN0cmFuZ2UgdGhpbmdzIGRvbid0IGhhcHBlbi4KCnNldHdkKCJ+L0RvY3VtZW50cy9DLXZpcmdpbmljYS1CU1NlcS9NZXRoeWxFeHRyYWN0L1ZDRnMvIikKc3lzdGVtKCJ2Y2YtbWVyZ2UgKi5neiA+IG1lcmdlZC52Y2YiKQoKc3lzdGVtKCJ2Y2Z0b29scyAtLXJlbGF0ZWRuZXNzIC0tdmNmIG1lcmdlZC52Y2YgLS1vdXQgcmVsYXRlZG5lc3MiKQpgYGAKCmBgYHtyfQoKc3lzdGVtKCJoZWFkIHJlbGF0ZWRuZXNzLnJlbGF0ZWRuZXNzIikKCmBgYAoKVGhhdCBsb29rcyBsaWtlIG15IHJlbGF0ZWRuZXNzIG1hdHJpeC4gTm93IG9mZiB0byBFeGNlbCB0byBtYWtlIHRoZSBjb21wbGV0ZSBtYXRyaXggZm9yIE1hY2F1Lg==