GemmaJ wrote:Ooohhh - Let me know if it's useful as I got that email as well but as I'd already got the information I needed I didn't explore any further. Sometimes I think I can know too much!!
Note, when uncompressed they all have a file extension of .vcf. This extension is also used for contacts in an address book. Obviously not the same format! The first file may have some utility. The second, not so much for me as no RS#'s listed. A vcf file reader would be helpful, though you can look at them like the below in a text editor. Likely more than I care about...
There are many more files I've yet to open.
First lines of one file:
##fileformat=VCFv4.2
##filedate=20200425
##source="beagle.25Nov19.28d.jar"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ci_d682aa54-5f87-4d6d-ac2c-7f8ee502a3ce_positions.txt.sorted
12 60219 rs371828716 G A . PASS DR2=0.00;AF=0.0007;IMP GT:DS 0|0:0
12 60317 rs566046722 C T . PASS DR2=0.00;AF=0.0038;IMP GT:DS 0|0:0.01
12 60473 rs112712197 C T . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 60474 rs537376773 G A . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 60492 rs558711391 T A . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 60654 rs574457226 G A . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 60663 rs541837560 T C . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 60734 rs557042443 G A . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 60760 rs572097088 C CA . PASS DR2=0.00;AF=0.1971;IMP GT:DS 0|0:0.39
12 60918 rs532304191 C CA . PASS DR2=0.08;AF=0.1757;IMP GT:DS 0|0:0.35
12 61107 rs186362565 G T . PASS DR2=0.00;AF=0.0015;IMP GT:DS 0|0:0
12 61161 rs569750441 A G . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
12 61172 rs535178008 G A . PASS DR2=0.00;AF=0.0042;IMP GT:DS 0|0:0.01
12 61329 rs575274757 C T . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
Another
##fileformat=VCFv4.2
##filedate=20200425
##source="beagle.25Nov19.28d.jar"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ci_d682aa54-5f87-4d6d-ac2c-7f8ee502a3ce_positions.txt.sorted
X 60020 . T TA,TAAC . PASS DR2=0.00,0.00;AF=0.0011,0.0130;IMP GT:DS 0|0:0,0.03
X 60026 . T C . PASS DR2=0.00;AF=0.0043;IMP GT:DS 0|0:0.01
X 60032 . T C . PASS DR2=0.00;AF=0.0043;IMP GT:DS 0|0:0.01
X 60034 . ACC AC,A . PASS DR2=0.00,0.00;AF=0.0000,0.0665;IMP GT:DS 0|0:0,0.13
X 60052 . T A . PASS DR2=0.00;AF=0.3644;IMP GT:DS 0|0:0.73
X 60060 . G C . PASS DR2=0.00;AF=0.0111;IMP GT:DS 0|0:0.02
X 60069 . T A . PASS DR2=0.00;AF=0.3644;IMP GT:DS 0|0:0.73
X 60071 . G A . PASS DR2=0.00;AF=0.0045;IMP GT:DS 0|0:0.01
X 60072 . G C . PASS DR2=0.00;AF=0.0034;IMP GT:DS 0|0:0.01
X 60072 . G C,T . PASS DR2=0.00,0.00;AF=0.0048,0.0809;IMP GT:DS 0|0:0.01,0.16
X 60112 . G C . PASS DR2=0.00;AF=0.0251;IMP GT:DS 0|0:0.05
X 60116 . C T . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
X 60153 . C G . PASS DR2=0.00;AF=0.0000;IMP GT:DS 0|0:0
X 60181 . G C . PASS DR2=0.00;AF=0.0023;IMP GT:DS 0|0:0
X 60184 . A G . PASS DR2=0.00;AF=0.0185;IMP GT:DS 0|0:0.04
X 60185 . T C . PASS DR2=0.00;AF=0.4499;IMP GT:DS 0|0:0.9