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4.9 years ago
giannkas1
•
0
I have a huge VCF file with all variants genotyped from a population of 95 individuals. I have filtered just for biallelic SNPs but now I need the Single-Dose Markers (SDMs) in order to build a genetic map. According to definition of Wu et al. 1992, a SDM is considered as a single-allele copy from only one of the parents of the cross, with a 1:1 segregation ratio, or the SDMs in both parents segregate in a 3:1 ratio. This is a fragment of the VCF file:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT P1 P2 P2_103 P2_107 P2_108
scaffold_1 1034 . G C 255 . NS=78;AN=2;MAF=0.07 GT:PL:GQ:DP:BSDP:ACN 0/1:656,94,398:255:31:0,19,12,0:4,6 1/1:1253,112,1:138:37:0,37,0,0:0,10 1/1:1302,115,1:141:38:0,38,0,0:0,10 1/1:1770,160,36:154:53:0,52,1,0:0,10 1/1:1768,154,0:255:51:0,51,0,0:0,10
scaffold_1 1557 . C T 50 . NS=82;AN=2;MAF=0.0 GT:PL:GQ:DP:BSDP:ACN 0/0:0,69,785:96:23:0,23,0,0:10,0 0/0:0,42,487:69:14:0,14,0,0:10,0 0/0:0,39,447:66:13:0,13,0,0:10,0 0/0:0,60,690:87:20:0,20,0,0:10,0 0/0:0,15,169:42:5:0,5,0,0:10,0
scaffold_1 3789 . C T 255 . NS=83;AN=2;MAF=0.06 GT:PL:GQ:DP:BSDP:ACN 0/0:1,299,3398:255:99:0,99,0,0:10,0 0/1:408,239,2287:138:79:0,67,0,12:8,2 0/1:344,208,2004:104:69:0,59,0,10:9,1 0/0:107,236,2479:255:78:0,75,0,3:10,0 0/1:309,217,2138:60:72:0,63,0,9:9,1
scaffold_1 4784 . A T 255 . NS=74;AN=2;MAF=0.04 GT:PL:GQ:DP:BSDP:ACN 0/0:0,244,2811:255:81:81,0,0,0:10,0 ./.:174,160,1669:0:53:48,0,0,5:10,0 0/0:51,88,929:69:29:27,0,0,2:10,0 0/0:36,172,1880:255:57:56,0,0,1:10,0 0/0:0,90,1043:117:30:30,0,0,0:10,0
Here I just show variants for 5 individuals. P1 and P2 are the parents.
Thank you so much in advance.
