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brentp
IndexError: list index out of range
HYE THERE I am using peddy to calculate PCA with command -m peddy -p 4 --plot --prefix 69_out PCA_data/69_without_N_imputated.vcf.gz PCA_data/69_without_N_imputed.plk.ped
after some initial start it is giving the following error. IndexError: list index out of range After reading a previous discussion I also modified the last row of the ped file, but still error is prevailing.
built installed from anaconda and git hub both are giving the same error. Kindly help me sorting it out
Hi, can you report the full error message and share your ped file? You can send it to me privately if you prefer.
Dear sure I will send you by morning. Sure
On Feb 12, 2018 11:43 PM, "Brent Pedersen" [email protected] wrote:
Hi, can you report the full error message and share your ped file? You can send it to me privately if you prefer.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/peddy/issues/39#issuecomment-364961847, or mute the thread https://github.com/notifications/unsubscribe-auth/AiuftH125wzk0fQc7UAWxu43KcTSUDzIks5tUFwHgaJpZM4SCV2s .
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Peddy requires that there is depth information associated with the variants. This is critical for filtering to high-quality genotype calls. You can add this artificially by setting e.g. AD=20,20.
Peddy could support cases where no genotypes have depths, but I have no plans to add that at this time as it will complicate the user-interface.
Thanks dear for Help. Just another sily question do I need to put this information in my ped file or adding it in my command line?
On Feb 14, 2018 5:33 AM, "Brent Pedersen" [email protected] wrote:
Peddy requires that there is depth information associated with the variants. This is critical for filtering to high-quality genotype calls. You can add this artificially by setting e.g. AD=20,20.
Peddy could support cases where no genotypes have depths, but I have no plans to add that at this time as it will complicate the user-interface.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/brentp/peddy/issues/39#issuecomment-365411598, or mute the thread https://github.com/notifications/unsubscribe-auth/AiuftB5z0IbZtS5VsnD5zxhpnYoqYi2qks5tUf-sgaJpZM4SCV2s .
-- http://ricecongress2018.irri.org/ The International Rice Research Institute http://irri.org is a member of the CGIAR http://cgiar.org System Organization, a global research partnership for a food secure future.
It would have to go in your VCF. Peddy only uses the first 6 columns of the ped/fam file to determine the expected relationships.