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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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vcf convert plink format #41

Closed feng0377 closed 4 years ago

feng0377 commented 4 years ago

The vcf file produced by MapCaller can't be converted into Plink formate file (map and ped), command: vcftools --vcf result.vcf --plink --out plink, Error: Require Genotypes in VCF file in order to output as PLINK. However, the problem don't happen in GATK software. The example vcf in MapCaller tutorial (ref.vcf and out.vcf) can't work too. Eagerly looking forward to response, thanks very much again！

hsinnan75 commented 4 years ago

Hi, thanks for the information. MapCaller does output genotype for snv and indels. I think it is an issue of formatting the attribute fields. I'll work on it and figure out how to modify the output. Thank you again.

feng0377 commented 4 years ago

Hi, hsinnan75, thank you very much. Looking forward to good news!

hsinnan75 commented 4 years ago

Hi, I've fixed the problem. Please download the latest version (v0.9.9.23). Please try again and let me know if there are any other problems regarding the use of MapCaller. Thank you!!

feng0377 commented 4 years ago

I am glad to receive your messenge，and I'm using it as soon as possible. Thank you again!