graphtyper

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Hi, Thanks for your wonderful tool. I plan to perform joint-calling on 1300 individuals (30X WGS) following the Manta + Svimmer + Graphtyper pipeline. I have run the Manta for...

jxcao98

Compiling graphtyper. Problem with include(`-I`) paths when compiling. /usr/include is ignored.

1

Hi again, after https://github.com/DecodeGenetics/graphtyper/issues/125 I'm trying to compile graphtyper . I got two problems when htslib was compiled. 1) For a strange reason `/usr/include` ( where there `zlib.h` is found)...

lindenb

Hi, I'm having some problems with the call SV process, here are my steps： ``` step1(for all samples): ${MANTA_INSTALL_PATH}/bin/configManta.py \ --bam ${input}/${bamsample}.mkdup.bam \ --referenceFasta $ref \ --runDir ${MANTA_ANALYSIS_PATH} \ --callRegions...

YiBenqiu

use clang++ make, fatal error: redefinition of 'this_compile_arch'

1

[root@eee release-build]# make -j4 graphtyper [ 3%] Performing build step for 'project_paw' [ 10%] Built target project_libdeflate -- Compilable archs are: NONE_NULL;ARM_NEON;ARM_NEON_FLT_SP;ARM64_NEON -- Runnable archs are: NONE_NULL;ARM_NEON;ARM_NEON_FLT_SP [ 19%] Built...

liuyong201811

Hi all! We were wondering if the SVs called by Graphtyper as LargeSVsize (Filter column) are considered as PASS. Thanks!

mplanasfelix

Hello! Thank you for this nice tool. I want to know if I can call SVs by genome assemblies instead of Manta, and then genotype SVs in the WGS population...

QianghuiZhu

problem about source code

1

Hello, I want to know if git clone is required to build from source code. It seems that htslib cannot be found in the tar package I downloaded.

HuangseYuanli

vcf_operations.cpp:525 Sample names are not unique

1

Dear Hannes I am using Graphtyper to call SNPs, it is quite convinent, while I got the error below vcf_operations.cpp:525 Sample names are not unique. The output VCF file will...

xuefenfei712

SNV discovery from PacBio or Nanopore data

4

Hi @hannespetur, Sorry I might have missed this somewhere. Does Graphtyper perform SNV discovery from PacBio or Nanopore data or is this something still under development? Thank you Kind regards,...

twesigomwedavid

HLA-Genotyping: <error> Converting "HLA-A*01:01:01:01" of size 17 to int failed

2

Good morning, I wanted to ask for some guidance regarding an issue I've been running into while genotyping structural variants using graphtyper. I am attempting a test-run of graphtyper v2...

Lukecassar21