Reference allel error in ped to vcf conversion
0
0
Entering edit mode
15 months ago
melania 2282 ▴ 100

Hi, In view to phase my data, i converted the ped file to vcf with plink, but the problem I have continuously a problem concerning reference alleles what is the best way to conver ped/bed file to vcf and align it to the reference genome to avoid the problem with refernce allele? thank you

SNP • 368 views
ADD COMMENT
0
Entering edit mode

Please provide more information. What is the source of your data? How was it processed? Which program(s) are you using?

ADD REPLY
0
Entering edit mode

Hi Kevin, My data come from genotyping with illumina chip, I tried to phase with eagle and shapeit but you have the same problem in both programs. For the vcf conversion I used this :

plink --file my file  --recode vcf --keep allele order

Thanks

ADD REPLY
0
Entering edit mode

What are the exact error and warning messages that you are receiving? Indeed, when using data from genotyping microarrays, not all SNPs will be aligned to the reference. You may have to obtain the library annotation for your array type in order to identify these, and/or make use of the --flip parameter in PLINK.

ADD REPLY
0
Entering edit mode

Yes how to get the vcf file from plink with the same allele order of the library oth array ? For example, for phasing from CHR1 , I have more than 30000 SNP excluded because of the ref/alt alleles difference between data and reference ?

Thanks

ADD REPLY
0
Entering edit mode

"What are the exact error and warning messages that you are receiving?"

ADD REPLY
0
Entering edit mode

Example for chr 1 output from shapeit:

  Reference and Main panels are not well aligned:
      * #Missing sites in reference panel = 33668
      * #Misaligned sites between panels = 707
      * #Multiple alignments between panels = 0
ADD REPLY
0
Entering edit mode

Please be aware that you need to run SHAPEIT like this: C: Phasing with SHAPEIT

What is your reference panel, by the way?

ADD REPLY
0
Entering edit mode

I used 1000 G as reference panel , the problem that If I will exclude problematic SNPs I will have to exclude about 30000 SNPs in chr1 for example ...

ADD REPLY

Login before adding your answer.

Traffic: 2325 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6