Issue with .map file generated using Plink software

Dear all,

I am working with the vcf file (generated using bcftools) to create a map file using plink software. The command i am using is

./plink --vcf sample.vcf --out sample --recode --allow-extra-chr

The output .map file looks like this

CM004562.1  .   0   1645
CM004562.1  .   0   4771
CM004562.1  .   0   4811
CM004562.1  .   0   4812
CM004562.1  .   0   5001
CM004562.1  .   0   5672
CM004562.1  .   0   5674
CM004562.1  .   0   5678
CM004562.1  .   0   5684
CM004562.1  .   0   5802

Kindly guide me where i am wrong? Why it outputs zero in the 3rd column?, and how to fix that?

Any help/suggestions would be highly appreciated.

Thanks in advance

genetic_map linuxos .map_file plink

• 514 views • link

written 4.4 years ago by taniamahmood38 •

0 answers

No answers yet.

More posts like this

Problem creating STRUCTURE inputs with PLINK
written 12 months ago by Begonia_pavonina •

I have formatting issues when preparing my data for STRUCTURE analysis. I am creating the input files for STRUCTURE, but unfortunately the .strct_in file produced …
Haploview linkage format .ped and .info file error
written 3.4 years ago by Nai •

I have chromsome specific vcf file, I have done tabix for indexing then perform plink with following command /plink --file Chr1 --recode HV --snps-only just-acgt …
Error: ##fileformat=VCFv4.2 does not exist
written 3.5 years ago by taniamahmood38 •

Hello everybody, I am using Pharmcat to preprocess my vcf file, and for this I am running this command python3 pharmcat_vcf_preprocessor.py -vcf NA12801.VCF But I …
Error in mapply(function(x, y)
written 4.3 years ago by taniamahmood38 •

Dear all, I am working on R and using the rehh package. I am converting the vcf file to an object of haplohh-class using the …
plink vcf
written 4.5 years ago by samuel

Hi, I'm a complete newbie using plink. I have the .bat .map and .ped files. I have then produced a vcf file with plink --file …
Selscan: ERROR: Alleles must be coded 0/1 only.
written 4.6 years ago by taniamahmood38 •

I am trying to run nsl statistics using selscan tool on a vcf file (created using freebayes). But i am getting this error ERROR: Alleles …
Make map file with recombination rate using plink?
written 5.2 years ago by curious

Trying to run [germline][1] and they use ped and map as input. They seem to have the 3rd map column for recombination rate not empty …
Dealing with half missing calls in ".ped" file
written 8.5 years ago by reza.jabal

I am trying to convert my VCF files to plink format for some downstream processing in PLINK. Since VCF half calls are coded as `"0/.", …
Recode to VCF with -a2-allele flag in PLINK
written 8.8 years ago by emyli •

Hi there, I generated a VCF using plink from .ped and .map files from a genotyping experiment as so: plink --file test --recode vcf --out …
plink 1.9 PED to VCF, SNPs differ on input and output files
written 10.8 years ago by stolarek.ir

Hi, I am using plink v 1.9 to convert my ped file to vcf with command: ./plink --ped file.ped --map file.map --recode vcf --out ped_to_vcf …