[strongside24]

ok sounds good. thank you! any instructions/info on how to get introns as well?

[laura]

the vcf to ped form and script should not skip any variants which are variable in the individuals you ask it to consider

Can you give a specific example of the variants you think it is missing and we will investigate

[strongside24]

I tried running it for mapk1. I entered the region I found through the browser and resulted 1619 variants, not the 6777. Thanks!

[laura]

Can you give me specific coordinates that you are using and let me know where your 6777 count comes from

When I look at our vcf file in ftp://ftp.1000genomes.ebi.ac.uk/vol1...ease/20110521/

laura@pg-trace-001[20110521]:tabix ALL.chr22.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz 22:22108789-22221970 | cut -f1-8

There is only 1591 sites and only 1532 of them are snps

thanks

[strongside24]

those are the results when i use the online converter. but we decided to use the script instead of the online converter so i wouldn't have to save the data onto my computer.

i'm trying to run the script again for the converter and it won't work. i downloaded the vcf to perl converter mentioned above and ran this script:

perl vcf_to_ped_converter.pl -vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz -sample_panel_file ftp://ftp.1000genomes.ebi.ac.uk/vol1...L.sample_panel -region 13:32889611-32973805 -population GBR -population FIN

and got this as a result:

Can't open perl script "vcf_to_ped_convert": No such file or directory

I'm assuming I installed/downloaded the script wrong. Am i correct?

[laura]

That would suggest the script isn't in the location where you are running the command from

[GenoMax]

i'm trying to run the script again for the converter and it won't work. i downloaded the vcf to perl converter mentioned above and ran this script:

perl vcf_to_ped_converter.pl -vcf ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz -sample_panel_file ftp://ftp.1000genomes.ebi.ac.uk/vol1...L.sample_panel -region 13:32889611-32973805 -population GBR -population FIN

Provide full path to where the script file was downloaded when you try to run the command

perl [COLOR="Red"]/full_path_to/[/COLOR]vcf_to_ped_converter.pl -vcf  ftp://ftp.1000genomes.ebi.ac.uk  .....