Katharine S. Walter

Hi, I'm wondering if folks might recommend a similar tool to extract SNPs from a multiple sequence alignment to generate an alignment of SNPs only? I am similarly running into...

Fantastic-thank you! I use this in combination with bcftools merge, to generate a fasta from VCF (for a haploid organism) as follows: bcftools +setGT --verbose --threads 4 ${vcf} -- --target-gt...

Hi, thank you, we considered that, however it seems strange that there would be such a long stretch (2.78 Mb) of confident homozygous ref calls on the X chromosome. Especially...

Hi, Thanks for all your work on this and apologies for the late response to your above help. Yes, we are very interested in the differences between the chrX calls...

Hi, I just wanted to follow up - are the chrX hg19 truth VCF calls reliable? Thank you!

We're also using your template: thank you for all your work making this resource! https://ksw9.github.io/

Hi, Thanks @jodyphelan for your documentation of this. I ran into the same problem with bcftools but it was fixed using the conda env file you posted above. Just FYI:...

Hi Jody, Yes, I think that’s it—I used the tb-profiler update_tbdb --match_ref command to update the chromosome name in my local tbdb. Thanks! From: Jody Phelan ***@***.***> Date: Thursday, September...