graphtyper

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regenotyped samples produces all Genptype (GT) with ./.

8

Hi, I have regenotyped 9000+ samples and gotten a small set of 72 samples with all genotype (GT) results to unknown (./.) The other 9000 samples have around 2400 structural...

Solyris83

core dumped

13

Hi: when i run graphtyper,it broken with the error,that means the computer node's cpu cant satisfy the graphtyper runnning? if so,when i run the script with 350 samples, what is...

koujiaodahan

One region in Trio has very slow genotyping

6

Using a large library of breakpoints, a job was submitted on the GIAB HG002 sample for each chromosome using 8 threads. Most chromosomes completed in under 8 hours except chromosome...

jjfarrell

FILTER=PASS but FT=FAIL1

3

Why is the filter a PASS for these 3 variants but the FT=FAIL1. Also what is the best software to compare these calls with the GIAB benchmark? The Ref All...

jjfarrell

Using a SV vcf from other callers than Manta

4

Hello, I'm trying to use Graphtyper as it seems to be fast and to scale well to many samples. Very easy to install and run so far.. but I'm unsure...

clairemerot

Minimum read length needed for genotype_sv?

5

I've been running tests on various data sets, and have had a few cases where `graphtyper genotype_sv` makes VCFs with almost every site having zero depth and a genotypes of...

martinghunt

Variant INFO/END position is before POS

3

Graphtyper can create variants where the END position is lower than POS. This results in a warning from bcftools concat: ``` Concatenating ./chr10/010000001-011000000.vcf.gz[W::vcf_parse] INFO/END=9321046 is smaller than POS at chr10:9321047...

seboyden

graphtyper genotyper_sv ：<error> No regions specified

3

Hi, I have 400 WGS samples and use manta+graphtyper2 to call SV. But I got an error. graphtyper genotyper_sv ： No regions specified. Either use --region or --region_file option to...

y1025i

Fatal error "FAI index has no entry" for GRCh38 HLA alt contig

6

Running graphtyper on GRCh38 with alt contigs, I get the following fatal error on chr6: ``` [constructor.cpp:159] FAI index has no entry for contig/chromosome 'HLA-DRB1*13' ``` Both the FASTA file...

seboyden

How do I connect the input and output of the three software (manta+svimmer+graphtyper)

1

Hi Manta has three variants file:diploidSV.vcf.gz ,candidateSV.vcf.gz and candidateSmallIndels.vcf.gz so ,should i merge the corresponding which file type(candidateSV.vcf.gz ? discard diploidSV.vcf.gz andcandidateSmallIndels.vcf.gz) to the config.sh of make_graphtyper_pipeline.sh? In addition, the...

koujiaodahan