John Didion

SNP calling and known genotypes (question + feature suggestion)

2

I have genotype array, WGS, and WGBS data for my samples. I am using this information to detect sample swaps. I find that Biscut genotype calls are highly concordant with...

It looks like right now vcf2bed only extracts information from the first sample column. It would be nice if you could 1) generate a separate output file for each sample...

Another SNP calling error

3

"a or b too big, or MAXIT too small in betacf: Numerical result out of range" Looks like a place where there just needs to be some exception handling.

Segmentation fault when SNP calling

10

I tried calling SNPs in 64 WGBS samples. All failed with segmentation faults at various points. Can you walk me through how to provide you with the debugging information you...

The MethylDackel (https://github.com/dpryan79/MethylDackel) README does a good job of describing mbias, and MethylDackel provides nice tools for identifying biased positions. I'm guessing you will provide something similar in Biscuit in...

Shores: the 2kb upstream and downstream of a CpG island (PMID 19151715) Shelves: the 2kb flanking shores (PMID 21839163) To illustrate: Ravines and Canyons are more recently described: Ravines: subclass...

Enable `create` to take input from stdin

1

It looks like `create` relies on the file extension to determine the type of input, which precludes using `/dev/stdin` as the input file. Since `create` doesn't have many filtering options,...

I am trying to build this in an ubuntu-based Docker image on an M1 mac and get the error: ``` #0 120.2 error[E0308]: mismatched types #0 120.2 --> /root/.cargo/registry/src/github.com-1ecc6299db9ec823/d4-hts-0.3.7/src/alignment/bamfile.rs:102:52 #0...

Do BAMs output by giraffe require indel realignment?

1

Based on the methods in the Draft Human Pan-Genome paper (https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1) it looks like BAM files surjected from giraffe graph alignments (which it appears can now be done directly by...

I am interested in using Octopus to generate candidate variants for [varlociraptor](https://varlociraptor.github.io/). Ideally I would like to skip the haplotyping, genotyping, and filtering steps (which would speed things up a...