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findallcoverageatposition output incorrect numbers

5

### Subject of the issue findallcoverageatposition output incorrect numbers ### Your environment * version of jvarkit: b0bbbff42 * version of java: openjdk version "1.8.0_275" OpenJDK Runtime Environment (build 1.8.0_275-b01) OpenJDK...

yliueagle

Gtf file with NCBI Ids for backlocate

2

This is a follow-up question on #170 issue. I am able to operate backlocate successfully after you provided the correct gtf file. Thank you so much for solving the issue...

pawarad

I used the tool biostar404363 to introduce artificial mutation SNV in bam, and the result I had (enclosed) showed actual AF tend to be lower than target AF at all...

ericaenjoy3

Are there default filters in sam2tsv? (general question; not an issue)

1

### Verify * if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue * the version of java java version "1.7.0_221" OpenJDK Runtime Environment (rhel-2.6.18.0.el7_6-x86_64 u221-b02) OpenJDK 64-Bit...

kac2053

MantaMerger running time too long and potential speeding up methods?

2

Hi jvarkit team, I am running MantaMerger for merging genome-wide structural variants of multiple ~6000 individuals to population-level SVs. However, it has been running since about three days ago. Is...

zjgbz

java.lang.RuntimeException: Not a diploid organism.

2

### Subject of the issue I got an error message, java.lang.RuntimeException: Not a diploid organism. I am working on a haploid organism. Does that mean that vcf to bam does...

CornilleAmandine

Vcf2Bam not recognizing sequence dictionary

4

Hi, I'm trying to use the tool vcf2bam from jvarkit and I have the following 2 files: `GRCh38_latest_genomic.fna` , and `00-common_all.vcf`. I used samtools faidx and also picard CreateSequenceDictionary to...

Mahmoudy96

Hi Pierre, Can i include a specific version of sam2tsv into my program and commit it to github repository? Thanks a lot for creating sam2tsv. Best, Huanle

Huanle

Biostar398854 does not work

9

### Verify I have followed the exact installation instructions specified at http://lindenb.github.io/jvarkit/Biostar398854.html. My java version is 11 (openjdk 11 2018-09-25, loaded in a guix environment) ### Subject of the issue...

AlBaarS

Not working with VCFs that have multiple chromosomes.

7

I have the 1000 genome phase 3 VCF's concatenated in a single VCF. I can successfully read it with [pyvcf](https://pyvcf.readthedocs.io/en/latest/), thus the file is consistent and healthy. When I try...

bambrozio