These are chat archives for dereneaton/ipyrad

11th
Apr 2017
Anna Mason
@AnnaMaryMason_twitter
Apr 11 2017 00:57
@isaacovercast thank you for the answer, yes I thought there would be a shift of 1 index but wanted to eb sure it is true for the whole file, so thank you! Concerning the .gphocs file I cannot find the pattern for matching sequences with the .loci file, additionally the first character of the sample names are missing so I am wondering if there is an issue with this file, would you like me to paste here the head of the loci and the .gphocs file?
@isaacovercast By the way, I am trying to get the consensus sequence for each loci and the coverage for each loci per sample, I can construct this by parsing the .loci and the .vcf files but you may have another easier suggestion?
Bohao Fang
@fangbohao_twitter
Apr 11 2017 09:00
Hi, all!
Bohao Fang
@fangbohao_twitter
Apr 11 2017 09:06
I just finished ipyrad (0.6.8) SNP calling based on reference method. However, the final vcf file does not have chromosome positon info, but locus position info. I am sure the reference genomoe has chrom position info.. So anyone knows how can I get Chromosome position info.?? Thank you!!
Anna Mason
@AnnaMaryMason_twitter
Apr 11 2017 11:10
@isaacovercast Hi again, I was comparing the .vcf file adn the .loci file and realised the loci in vcf go from 7 to 17988 but my loci file goes from 3 to 17992, do you know how to explain this discrepancy? Thank you