Hi Guy,
Tassel will output in a variety of formats including Hapmap, Hapmap Diploid, HDF5, VCF, and some others. After stringent filtering, I am left with ~750 taxa and 17000 SNPs.
Hapmap output looks like this:
rs# |
alleles |
chrom |
pos |
strand |
assembly# |
center |
protLSID |
assayLSID |
panelLSID |
QCcode |
160696 |
160944 |
161113 |
S01_18244 |
A/G |
1 |
18244 |
+ |
NA |
NA |
NA |
NA |
NA |
NA |
A |
A |
N |
S01_54667 |
C/T |
1 |
54667 |
+ |
NA |
NA |
NA |
NA |
NA |
NA |
C |
C |
C |
S01_62404 |
T/G |
1 |
62404 |
+ |
NA |
NA |
NA |
NA |
NA |
NA |
G |
T |
G |
Diploid hapmap looks like this:
rs# |
alleles |
chrom |
pos |
strand |
assembly# |
center |
protLSID |
assayLSID |
panelLSID |
QCcode |
160696 |
160944 |
161113 |
S01_18244 |
A/G |
1 |
18244 |
+ |
NA |
NA |
NA |
NA |
NA |
NA |
AA |
AA |
NN |
S01_54667 |
C/T |
1 |
54667 |
+ |
NA |
NA |
NA |
NA |
NA |
NA |
CC |
CC |
CC |
S01_62404 |
T/G |
1 |
62404 |
+ |
NA |
NA |
NA |
NA |
NA |
NA |
GG |
TT |
GG |
Any help would be appreciated.
Thanks,
Brian