tomahawk

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compilation issue

3

I'm having trouble compiling this on Linux. I tried both your dockerfile `docker build -t tomahawk .` and on our local system (centOS7.8 with gcc 7.3.1) and received the same...

jaredo

core dump error on import

20

Hi, I'm trying to import a bcf file that was generated by first converting a GATK vcf to bcf with bcftools. I'm getting the following error: ``` Program: tomahawk-beta-0.7.1 (Tools...

peterdfields

Getting this error: tomahawk: error while loading shared libraries: libhts.so.2: cannot open shared object file: No such file or directory Hoping someone has a fix.

juliandwillett

First of all, thank you for the amazing software! I was able to convert all bcf files but one, so I guess the input file is the problem. Nonetheless, the...

soulsacross

Dear mklarqvist,  I think my input vcf is ok, but why the software indicate `not SNP` Best, Han

laserhsu

Clumping and pairwise LD for specified SNP lists

2

I was alerted to your package recently and it looks extremely valuable, congratulations! I did have a couple of feature requests, apologies if this is already implemented I didn't see...

explodecomputer

htslib has breaking changes, here using a commit used in the most recent published tomahawk docker image

juhis

Hi, Is there a citation/reference for the math tomahawk does on unphased genotypes to compute LD?

JesseGarcia562

Add a document detailing how to transmute `TWO` files into [HiGlass](https://higlass.io/)-compatible formats such as [Cooler](https://github.com/mirnylab/cooler).

mklarqvist

Hi, I'm trying to import a vcf file [tmp_subset.vcf.gz](https://github.com/mklarqvist/tomahawk/files/15482313/tmp_subset.vcf.gz) and getting the following error: $ tomahawk import -i out/tmp_subset.vcf -o tmp/test.twk Program: tomahawk-beta-0.7.1-dirty (Tools for computing, querying and storing LD...

skellyfalke