shuaiwang2

Hi, @nalinigans By using the same data, procedure and software like @baoxingsong, I found that the super-indel(the length is 34461688 at chromosome 9; 10668738 at chromosome 10 respectively) lead to...

@nalinigans ,I have put the command for chromosome 9 and chromosome 10 is similar, thanks. ``` gatk --java-options "-Xmx40g" GenotypeGVCFs -R /home/xuql/copyNAM/B73/Zm-B73-REFERENCE-NAM-5.0.fa -stand-call-conf 0 -ploidy 1 -V gendb:///home/xuql/copyNAM/NAM_out_gatk9_1 -O /home/xuql/copyNAM/gatk93.vcf.gz...

thanks for your questions. Convert MAF file to VCF file with [tassel](https://bitbucket.org/bucklerlab/practicalhaplotypegraph/wiki/UserInstructions/CreatePHG_step2_MAFToGVCFPluginDetails.md) is the best way. The plugin can run directly from tassel-5-standalone as follow. this is an example to...