Question: Error while creating .geno file with LEA
0
gravatar for beausoleilmo
3.0 years ago by
beausoleilmo280
McGill University
beausoleilmo280 wrote:

I'm using LEA to create a .geno file from a VCF. But I get this error:

vcf2geno(input.file = "output_simple_header.vcf")
Error while reading SNPs informations at line 255031.

Is there a way to get around this. I've looked at this line and everything seems normal (see below).

Is there another software to create a .geno file?

sed -n '255031{p;q}' output_simple_header.vcf

scaffold11  491359  .   T   C   999 .   DP=20550;VDB=0;SGB=-3001.55;RPB=3.1581e-12;MQB=0;MQSB=1.76368e-23;BQB=2.07132e-26;MQ0F=0;AF1=0.5;G3=5.35839e-16,1,8.61906e-22;HWE=8.6655e-31;AC1=96;DP4=9591,337,10055,92;MQ=25;FQ=999;PV4=5.76122e-36,1.05141e-12,0,0.0256033  GT:PL:DP:SP:GQ  0/1:101,0,156:250:0:99  0/1:116,0,173:249:0:99  0/1:70,0,149:162:0:73   0/1:105,0,169:250:0:99  0/1:116,0,162:250:0:99  0/1:101,0,167:250:0:99  0/1:82,0,198:246:6:85   0/1:93,0,135:154:0:96   0/1:81,0,170:249:0:84   0/1:108,0,158:249:0:99  0/1:100,0,160:249:0:99  0/1:96,0,142:172:3:99   0/1:120,0,158:180:79:99 0/1:116,0,137:238:0:99  0/1:105,0,147:250:0:99  0/1:133,0,170:230:5:99  0/1:80,0,164:248:0:80/1:121,0,157:250:0:99  0/1:140,0,180:247:0:99  0/1:68,0,139:78:0:71    0/1:102,0,166:209:0:99  0/1:114,0,150:249:0:99  0/1:76,0,211:203:54:79  0/1:122,0,167:250:0:99  0/1:102,0,166:248:0:99  0/1:104,0,138:249:0:99  0/1:89,0,169:206:0:92   0/1:94,0,142:157:0:97   0/1:114,0,133:250:0:99  0/1:122,0,162:196:6:99  0/1:134,0,252:225:44:99 0/1:118,0,162:249:0:99  0/1:99,0,161:248:0:99   0/1:121,0,157:247:0:99  0/1:66,0,170:212:0:69   0/1:79,0,170:249:0:82   0/1:133,0,239:241:8:99  0/1:99,0,161:223:0:99   0/1:81,0,154:142:12:84  0/1:123,0,141:250:0:99  0/1:91,0,146:166:0:94   0/1:116,0,171:249:0:99  0/1:103,0,153:167:0:99  0/1:82,0,228:243:16:85  0/1:95,0,152:141:66:98  0/1:84,0,150:136:0:87   0/1:88,0,138:133:0:91   0/1:90,0,140:152:0:93   0/1:107,0,135:250:0:99  0/1:88,0,148:143:0:91   0/1:78,0,128:61:0:81    0/1:82,0,84:249:0:83    0/1:65,0,187:248:3:68   0/1:70,0,140:99:0:730/1:130,0,253:186:69:99 0/1:104,0,160:250:0:99  0/1:99,0,134:250:0:99   0/1:76,0,143:126:0:79   0/1:91,0,161:212:0:94   0/1:82,0,161:195:0:85   0/1:99,0,187:214:3:99   0/1:153,0,183:226:3:99  0/1:89,0,118:141:0:92   0/1:129,0,189:246:0:99  0/1:75,0,140:69:0:78    0/1:100,0,174:250:0:99  0/1:72,0,131:78:0:75    0/1:105,0,150:200:0:99  0/1:107,0,132:248:0:99  0/1:106,0,146:220:0:99  0/1:113,0,132:250:0:99  0/1:112,0,207:139:50:99 0/1:116,0,144:147:0:99  0/1:58,0,158:249:0:61   0/1:141,0,159:144:41:99 0/1:99,0,153:176:0:99   0/1:65,0,178:248:0:68   0/1:123,0,156:247:0:99  0/1:158,0,216:242:0:99  0/1:126,0,154:248:0:99  0/1:158,0,227:221:49:99 0/1:93,0,135:181:0:96   0/1:109,0,154:247:0:99  0/1:104,0,146:249:0:99  0/1:135,0,254:242:0:99  0/1:73,0,155:184:0:76   0/1:108,0,123:250:0:99  0/1:79,0,140:127:0:82   0/1:116,0,147:250:0:99  0/1:79,0,179:249:0:82   0/1:123,0,222:242:3:99  0/1:104,0,118:193:0:99  0/1:116,0,128:249:0:99  0/1:109,0,127:188:0:99  0/1:190,0,196:200:28:99 0/1:103,0,151:211:0:99
geno lea vcf • 983 views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.0 years ago by beausoleilmo280
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