Best practices for converting plink bed bim fam to geno snp ind

[geneanalyst]

Is there currently a best practice for adding plink bed bim fam samples to geno snp ind datasets.

I've always 1st converted geno snp ind to plink using convertf , merged all plink data in plink, then converted bed bim fam to ped map pedind and back to geno snp ind using convertf.

Sometimes I feel this is not the best way to do it though.

Also, FYI plink doesn't preserve allele order and I wasn't sure if allele order in snp files is important to AF calculations, so I have as a matter of practice always re-aligned allele order in snp files (messed up by conversions from plink) to match dbSNP and ensure that col 5 is REF and col 6 is ALT in snp file

[bumblenick]

The way I do this is use convertf to move the initial plink files and then use mergeit But flipping the count/variant alleles matters You need to get that right Tip: include human reference in each data set Makes sorting out flipping easy and see also polarize feature in convertf Nick

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On Mar 6, 2021, at 3:26 PM, geneanalyst ***@***.***> wrote:  Is there currently a best practice for adding plink bed bim fam samples to geno snp ind datasets. I've always 1st converted geno snp ind to plink using convertf , merged all plink data in plink, then converted bed bim fam to ped map pedind and back to geno snp ind using convertf. Sometimes I feel this is not the best way to do it though. Also, FYI plink doesn't preserve allele order and I wasn't sure if allele order in snp files is important to AF calculations, so I have as a matter of practice always re-aligned allele order in snp files (messed up by conversions from plink) to match dbSNP — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[geneanalyst]

Thanks. Do you have a par file I can use for mergit? I didn't see any commands for it.

Ok, I was concerned that that the code looks to col 6 of snp for ALT and to calculate AF. As a matter of practice I use a script to re-import REF and ALT into col 5 and 6 of snp from Hg Reference Genome

[bumblenick]

I didn't put a sample par file for mergeit in the documentation (which is in .../converff/README) and I guess I should. Read the documentation carefully and try and use strancheck: NO if possible Nick

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On Sat, Mar 6, 2021 at 8:55 PM geneanalyst ***@***.***> wrote: Thanks. Do you have a par file I can use for mergit? I didn't see any commands for it. Ok, I was concerned that that the code looks to col 6 of snp for ALT and to calculate AF. As a matter of practice I use a script to re-import REF and ALT into col 5 and 6 of snp from Hg Reference Genome — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77B2EIHL6EBUERGX7JALTCLMK5ANCNFSM4YXCM2IA> .