These are chat archives for dereneaton/ipyrad

11th
May 2018
Gazza007
@Gazza007
May 11 07:36
@isaacovercast That key for the BWA parameters could come in very handy (although I'd still prefer to use nucmer for mapping). At what step of the pipline would you feed in the modified json file?
Bruno de Medeiros
@brunoasm
May 11 12:28
@isaacovercast Hi Isaac, thank you for your response. I am doing 'reference'. Most reads map to the reference, and I see there are bam files for each sample. In the VCF output I see the fasta file I gave as reference in the header, but chromosome IDs are "locus_1", "locus_2", not sequence names in the original fasta. I would like to map SNPs back to their original coordinates in the reference genome.
Isaac Overcast
@isaacovercast
May 11 16:05
@Gazza007 If you modify the json file you'll just have to re-run from step 3. I'll check out nucmer as well.
@brunoasm Hmm, weird, I'll check it out, this worked last time I looked at it.... I'll get back to you.