Haploview and plink

Question

[Nai]

When I executed plink to get .ped and .info file then IT generated only for 8 chromosomes out of 22, X, Y and M. Kindly help to get all chromosomes.

1. When I am uploading .ped and .info file in Haploview.jar then it is showing loading 0% for creating hapmap

Answer 1

[Kevin Blighe]

HaploView is intended for specific genomic intervals where you want to define tagging SNPs, compute linkage disequilibrium, etc. It will not be able to load an entire genome's worth of information ,even if from a low density SNP array. That is too much information and it will 'crash' the computer, or just never load.

For simple usage of HaploView coming from PLINK, please see my 2 previous answers:

• How do I compute ld blocks from the hapmap ld_data?
• Manhattan plots and linkage disequilibrium heatmap

Kevin

[Nai]

Thank you Kevin.

[Nai]

If I would like to extract some region on specific chromosome from vcf file. May I know how to do it.

[Nai]

Hi Kevin,

When I tried with extracted region .ped and .info file. Then Haploview gives an error "File contains zero valid indiviuals"

[Kevin Blighe]

Can you show some status messages output by PLINK when you do this? - not just the error message

[Nai]

This msg was given by Haploview.jar after loading .ped and .info file.

[Kevin Blighe]

Can you please show the output from PLINK, and the command(s) used. Thank you!

[Nai]

Hi,

To generate .ped and .map

vcftools --vcf all_sample_no_indel.recode.vcf --plink --out all

To convert .ped as input of haploview

./plink --file all --recode HV --snps-only just-acgt --out hap_out

Output of .ped and .info:

head -n 1 *.ped
G G T T A A 0 0 T T 0 0 0 0 C T T T C C C C 0 0 G G T T A A 0 0 0 0 0 0 0 0 G G 0 0 G G C T A A A A 0 0 G G 0 0 0 0 G G 0 0 0 0 0 0 0 0 T T G G 0 0 G G T T C T A A A A 0 0 T C A A C C G G 0 0 C C 0 0 0 0 0 0 T T C C C C 0 0 0 0 0 0 0 0 0 0 0 0 T T A A 0 0 0 0 T T C C 0 0 G G 0 0 G G A A 0 0 0 0 0 0 C C A A 0 0 G G 0 0 G G 0 0 C G 0 0 T T C C 0 0 0 0 G G G G 0 0 0 0 0 0 0 0 0 0 A A G G A A 0 0 G G C C 0 0 C C 0 0 C C T T C C C A 0 0 T T C C T G A G A G G G T T G G A A C C G G T T T T A A C C 0 0 A T C C 0 0 G G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 C C 0 0 G G 0 0 0 0 0 0 0 0 G G T T 0 0 0 0 T T G G G G G G 0 0 G G G A A G G G 0 0 A A G G T T A A 0 0 0 0 A A A A C C A A G G G G C C 0 0 A A 0 0 G G A A 0 0 0 0 0 0 G G A G 0 0 C C 0 0 0 0 0 0 0 0 C C 0 0 G G 0 0 T T T T 0 0 A A 0 0 0 0 G G 0 0 0 0 T T 0 0 0 0 T T T T C C A A T T 0 0 G G C C T C 0 0 0 0 C C 0 0 0 0 A A C C T T 0 0 0 

head -n 10 *.info
chr1:10165  10165
chr1:10444  10444
chr1:10446  10446
chr1:10452  10452
chr1:10492  10492
chr1:17407  17407
chr1:17408  17408
chr1:17452  17452
chr1:17516  17516
chr1:17519  17519

[Kevin Blighe]

The PED file is invalid. The first 6 columns should be:

Family ID
Individual ID
Paternal ID
Maternal ID
Sex (1=male; 2=female; other=unknown)
Phenotype

Note that you can read VCF into PLINK directly using the --vcf parameter. For example:

plink --noweb \
      --vcf myvariants.vcf \
      --keep-allele-order \
      --vcf-idspace-to _ \
      --const-fid \
      --allow-extra-chr 0 \
      --split-x b37 no-fail \
      --make-bed \
      --out myvariants ;

[Nai]

Here it will take snp as well indels.

[Nai]

By this I will get .ped and .info file?

[Nai]

Output of above command with bed, bim and fam files. Total genotyping rate is 0.973862. 6283247 variants and 21 people pass filters and QC. Note: No phenotypes present.

[Nai]

Dear Kevin,,

I would like to extract some chromosome region from vcf file (For extracting I am trying tabix) then I would like to look its hapmap.