Much appreciated for the remake of the video. it was incredibly detailed and thorough, and it has helped me immensely. While searching for information on 'converting plink files to vcf files' elsewhere, I often received simple instructions to use the --recode command. However, your emphasis on the reference genome issue was crucial. I believe this aspect, which you highlighted, is vital for the genome imputation work I am about to undertake. Your insights have truly expanded my understanding. Thanks again!
@GenomicsBootCamp, thank you very much for this nice video. I was wondering what your thoughts are about INDELs. If you use plink to convert to vcf, INDELS will be given as an "I" and "D". These will break multiple tools downstream. I was wondering how you would handle this situation.
Always rewatching, Professor, my VCF file has family names and other information (FID, GPS, Age, Sex, etc.) included in the metadata section. How do I extract and associate each piece of information with the individual ID genotype, because I would like to convert this VCF into plink files.? Please advise.
"At least one VCF allele code violates the official specification" A warning message after I ran --recode vcf, what could be the problem here and how do I solve it?
Warning messages are usually non-critical issues, and most of the time it is ok to go forward. Still, checking the source of the problem is advised. Here, probably one or more loci do not have the expected A, T, G, C codes. Or you might have other variants, such as indels in your VCF, that are causing this warning? If you are interested in SNPs, I would use the --snps-only PLINK option in this or follow up step www.cog-genomics.org/plink/1.9/filter#snps_only
@@GenomicsBootCamp thankyou so much for your response, i really needed it. Further on the question, i also noticed that my vcf file does not have chromosomes, and positions yet ped and map files have them. Is there a step i jumped?
Much appreciated for the remake of the video. it was incredibly detailed and thorough, and it has helped me immensely. While searching for information on 'converting plink files to vcf files' elsewhere, I often received simple instructions to use the --recode command. However, your emphasis on the reference genome issue was crucial. I believe this aspect, which you highlighted, is vital for the genome imputation work I am about to undertake. Your insights have truly expanded my understanding. Thanks again!
Thank you Professor Gabor for providing such an informative video.
You are welcome!
@GenomicsBootCamp, thank you very much for this nice video. I was wondering what your thoughts are about INDELs. If you use plink to convert to vcf, INDELS will be given as an "I" and "D". These will break multiple tools downstream. I was wondering how you would handle this situation.
Hello respected Sir,
Please make a video on how to run XPCLR? or just show how to convert vcf file into .geno format?
Always rewatching,
Professor, my VCF file has family names and other information (FID, GPS, Age, Sex, etc.) included in the metadata section. How do I extract and associate each piece of information with the individual ID genotype, because I would like to convert this VCF into plink files.?
Please advise.
How can I convert SNP data of bi-allelic nucleotide bases (AA, AG, GG, CC, etc.) and recode them as 0, 1, 2, and NA format, without reference allele?
Can you share a video for converting CSV to vcf, hapmap and plink please?
"At least one VCF allele code violates the official specification" A warning message after I ran --recode vcf, what could be the problem here and how do I solve it?
Warning messages are usually non-critical issues, and most of the time it is ok to go forward. Still, checking the source of the problem is advised.
Here, probably one or more loci do not have the expected A, T, G, C codes. Or you might have other variants, such as indels in your VCF, that are causing this warning?
If you are interested in SNPs, I would use the --snps-only PLINK option in this or follow up step
www.cog-genomics.org/plink/1.9/filter#snps_only
@@GenomicsBootCamp thankyou so much for your response, i really needed it. Further on the question, i also noticed that my vcf file does not have chromosomes, and positions yet ped and map files have them. Is there a step i jumped?
Sir, please provide a video to convert .VCF file to PLINK binary format
Hi, already done that: ua-cam.com/video/EJDknrHAkXs/v-deo.html