Error while creating .geno file with LEA

Question

[beausoleilmo]

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

[brallen]

Hello! I realize this post is 3.5 years old but I'm running into the same issue. By any chance do remember what may have caused it? Best, Brian.

[beausoleilmo]

I actually never got it to work...

Answer 1

[brallen]

Hello, no worries. Thanks for your response! I ended up emailing the software developer. Since the VCF format has changed since the software was developed, they suggested "using VCFTOOLS to convert the vcf files as PED. Then the ped format can be converted into .geno and .lfmm with ped2geno or ped2lfmm. Note that .lfmm can be obtained from .ped directly by removing the first (six) columns (.lfmm = genotypes in rows, no additional info)."

Posting here for anyone else who might run into the same problem.

[beausoleilmo]

Thanks for the follow up!

[beausoleilmo]

A friend of mine told me she used the function vcf2lfmm which will create a .lfmm and .geno file. https://www.rdocumentation.org/packages/LEA/versions/1.4.0/topics/vcf2lfmm.