1
0
Entering edit mode
26 days ago
Nai • 0

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.

Plink Haploview and • 617 views
0
Entering edit mode
26 days ago

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.

Kevin

0
Entering edit mode

Thank you Kevin.

0
Entering edit mode

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

0
Entering edit mode

Hi Kevin,

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

0
Entering edit mode

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

0
Entering edit mode

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

0
Entering edit mode

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

0
Entering edit mode

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

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

0
Entering edit mode

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 ;

0
Entering edit mode

Here it will take snp as well indels.

0
Entering edit mode

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

0
Entering edit mode

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.

0
Entering edit mode

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.