[AsoBioInfo]

Hello. I chanced across this forum and I wonder if I can ask a rather naive question. I recently used PLINK/ Haploview for understanding the data of the highly ranked SNPs in a GWAS analysis. I had planned to visualize my SNPs in LD blocks [and their proximity to genes of interest[, by using Haploview. Additionally, I used dbSNP to confirm the proximity of my SNPs to genes of potential interests.

Curiously enough, no matter how hard I have tried, I cannot get Haploview to show the same genes, that I can visualize when using dbSNP. I have tried repeatedly but with no satisfactory breakthrough. I would be so grateful if someone could have some suggestions on what I may be doing incorrectly.

I can also give a list of sequential steps [ as to what I am doing that is giving different results]

Thankyou for taking the time to read my question.

A.Z

Can't understand your question. What exactly you want to do with your data? Can you elaborate it!

[alizaid12]

Hello and thanks for the replies. I am sorry for not expressing my thoughts carefully in the earlier email. I have made a little powerpoint showing with 3 seections. Please see attached ppt file
--[section 1] the steps of my workup in Haploview and
--[section 2] the LD block results I am trying to obtain, to get try and get [this is an example]
--[section 3], the problem I am facing repeatedly

I have tried all the possible combinations of Haploview [see the slides of section 1] but I am not able to get a result for rs41363947 [the top ranked SNP in my list]. For that matter, for all my other high ranked SNPs, although some genes are seen in dbSNP, but I cannot confirm my results in Haploview

Thank you

Ali

[alizaid12]

Also, I saw the attached files from Gringer san. I would very much like to read your paper [if already published, as it may very well be a good reference paper for my PhD thesis and subsequent actual paper]. If not yet published, please do let me know. I think your methods section would be very good reading.

All the 3 files attached your provided are good[especially the file titled maoA_LD_with_VNTR.pdf is how I would probably wish to show the results for each one of the top 10 SNPs from my high ranked SNP list].

I welcome your suggestions / comments

[gringer]

So, at a guess, you're analysing the hapmap data surrounding a particular SNP (i.e. downloading from within Haploview, rather than your own data), which simplifies things a bit.

In terms of getting a good picture, I'd suggest downloading an SVG version of the data track from the Hapmap website (Hapmap Genome Browser, click on the '[High-res Image]' link just above the search bar), and combining that with an SVG export from Haploview. You can then import both images into Inkscape or Illustrator and change text sizes to suit your preferred layout. It's a bit fiddly to edit -- I think I manually removed all the grey blocks around the image, but produces a much nicer result than a bitmap image.

The official page for my thesis is here. The unofficial location for my thesis is http://gringer.org/thesis.pdf. There's a paper on the MAOA gene (based on one of the chapters in my thesis) which has just been accepted for publication, but I don't yet have a link for that.

[gringer]

I have tried all the possible combinations of Haploview [see the slides of section 1] but I am not able to get a result for rs41363947 [the top ranked SNP in my list]. For that matter, for all my other high ranked SNPs, although some genes are seen in dbSNP, but I cannot confirm my results in Haploview

It may be that your favourite SNP is flagged as invalid by Haploview for a number of reasons. It is possible to enable it so that it shows up in the LD plot, as I mentioned in a previous response:

Then you probably have markers that have been flagged to be ignored for some reason. Go to the marker tab and see if there are any red fields for those markers (this will explain why the marker was excluded. Check the 'rating' box for your markers, and they should be included and appear in the LD plot.

[alizaid12]

Gringer san. I just saw messages. I will definately be working on this. I would like to post back my progress on the forum again. Thankyou so much for taking time out to help. I really appreciate it.

Much regards from Tokyo...;-]

[gringer]

どういたしまして。You're welcome.

[alizaid12]

Thanks ;-]. I downloaded inkscape and will try to see how I can work it. Will post back soon.

Have a great day

[ymc]

I use beagle for phasing. It seems like it is the tool 23andme used in their papers.

[gringer]

I use beagle for phasing. It seems like it is the tool 23andme used in their papers.

I think you meant to post in this thread:

http://seqanswers.com/forums/showthread.php?t=16777

[neio1114]

Generating .ped and .map file

I am trying to use merlin for pedigree analysis
I have obtained ~100 variants(VCF)
looks like ped file can be generated from vcf file by vcftools.
I cannot figure out how to generate .map file from vcf..
Actually, I cannot really figure out how to use merlin if I only have vcf file..
It will be awesome if someone could save me from this

[dheeraj]

Hi,

Not sure if this is the right place to post this error while using Haploview. I have a vcf file and I have converted it to PED and MAP files by vcftools. Then I tried to load it into haploview and it throws this error "For any marker, an individual's genotype must be only letters or only". I have checked the vcf file and ped file. Everything looks fine. Please let me know, if you have any ideas in solving this problem. Thanks in advance.

Dheeraj.

[gringer]

Without knowing what your input file looks like, there's not much that can be done to help. If you have a linux command line available, then the following should give an idea of whether the file has odd-looking input:

perl -pe 's/^\s+//;s/\s$//;s/[ \t]+/\t/g' <input_file.txt> | cut -f 7- | perl -pe 's/\t/\n/g' | sort | uniq -c

Translation: strip trailing and leading spaces, convert spaces to tabs, remove the first 6 columns, convert tabs to line breaks, count unique lines

Output should be something like the following:

    122 0
   1826 1
   1380 2
   1703 3
   1185 4

[dheeraj]

Without knowing what your input file looks like, there's not much that can be done to help. If you have a linux command line available, then the following should give an idea of whether the file has odd-looking input:

perl -pe 's/^\s+//;s/\s$//;s/[ \t]+/\t/g' <input_file.txt> | cut -f 7- | perl -pe 's/\t/\n/g' | sort | uniq -c

Translation: strip trailing and leading spaces, convert spaces to tabs, remove the first 6 columns, convert tabs to line breaks, count unique lines

Output should be something like the following:

    122 0
   1826 1
   1380 2
   1703 3
   1185 4

Hi,

Thanks for your reply, but actually I fixed it. The problem was the using the ped file from vcftools. I had to use the vcf to ped converter from 1000genomes website.

cheers,
Dheeraj

[dheeraj]

Hi,

I am trying to identify the SNPs that are in LD with one of the rare SNP identified in our study in one family in a particular gene. So, I want to use Haploview for LD calculations, I have a multisample VCF file with the genotypes of all the family members. I have few questions regarding the analysis:
Can I use haploview to do the analysis without phasing the genotypes ??
If phasing is required can I use BEAGLE to do the phasing and impute the missing parental genotypes at the same time ??

Or any other suggestions ??

Please let me know. Thank you very much in advance.

Dheeraj.