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User: A.Mubashir

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Posts by A.Mubashir

<prev • 8 results • page 1 of 1 • next >
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How to convert allele column of HapMap genotype data format into REF and ALT columns of VCF format?
... How can we convert Allele column of Hapmap SNP genotype data format into ALT and REF columns of VCF format? In HapMap format, there is a column with header name allele. But in the vcf format, ALT and REF headers are present instead of allele headers like in hapmap. ...
genome snp sequencing written 5 weeks ago by A.Mubashir • 0
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How to impute missing SNPs of genotypic data of plant species, without having HapMap reference panel?
... hello all, I have a SNP genotype data of 228 accessions of cotton, on which I want to do GWAS. The genotype data has a lot of missing SNPs, which should be imputed. I have calculated genotyping rate in plink, which is 0.72. My goal is to do GWAS. The genotype data is already published, and I down ...
genome R snp written 6 weeks ago by A.Mubashir • 0
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Comment: A: Unrecognized flag in Plink2
... I got it, thank you for your quick response ...
written 10 weeks ago by A.Mubashir • 0
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Unrecognized flag in Plink2
... Hello all, I have been trying to calculate linkage disequilibrium on plink2 in linux, but it is constantly showing an error, following is my command and error plink2 --file hapmap1 (this is the command that I typed) PLINK v2.00a3LM 64-bit Intel (31 Aug 2020) www.cog-genomics.org ...
genome snp written 10 weeks ago by A.Mubashir • 0
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Comment: A: Which Genotype file format is it?
... Thank you so much for your quick response. However, i answered very late, and sorry for that. I read a lot of stuff and figure out that the genotype file that i have, doesnot follow any format. Actually, it is neither vcf nor any other format. I have converted it in hapmap, vcf and plink format. A ...
written 12 weeks ago by A.Mubashir • 0
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Which Genotype file format is it?
... Chromosome Position RefBase AltBase MAF RefBaseNum AltBaseNum Sample 1 Sample2 Sample3 I am confused about this format. I have downloaded it from an online database. I looks like vcf format, but it is not supported by any software. ...
genome snp written 3 months ago by A.Mubashir • 0
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Comment: C: Filtering already published SNP data
... Thanks for your kind response and suggestions. ...
written 3 months ago by A.Mubashir • 0
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Filtering already published SNP data
... Hello, I want to do GWAS on 200 accessions of a plant. The SNP data has already been published and I just downloaded it from an online database. Since, the SNP data has already been processed by the person, who used it to conduct GWAS on a different trait and got it published in a well reputed ...
snp written 3 months ago by A.Mubashir • 0

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