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Before there is webpage for how to convert plink ped format to vcf
format. But it seems that this link disappeared.
Thank you very much in advance.
You cannot use the GATK to convert from ped to VCF. The link just advised people to use PlinkSeq.
I wrote a small script that uses plink to do the PED to VCF conversion:
The trickiest part, at least with my dataset, was orienting calls back to the reference strand. Hope this is helpful.
Thanks chapmanb for the script!
For me, the script seems to be running into an error partway through chromosome 1:
Traceback (most recent call last):
File "/home/chongm/Scripts/plink_to_vcf_chapmanb.py", line 158, in
File "/home/chongm/Scripts/plink_to_vcf_chapmanb.py", line 29, in main
File "/home/chongm/Scripts/plink_to_vcf_chapmanb.py", line 148, in fix_nonref_positions
parts = fix_vcf_line(parts, ref_base)
File "/home/chongm/Scripts/plink_to_vcf_chapmanb.py", line 97, in fix_vcf_line
elif ref_base != ref and complements[ref] == ref_base:
Any suggestions on how to fix this?
Actually you know what I realized that my chip data had some deletions and insertions which might be problematic...