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It seems that `bcftools concat` will segfault if the files it's combining have only headers:
```
$ bcftools concat -d exact -a -o combined.vcf.gz -O b --threads 1 bar.vcf.gz foo.vcf.gz
Checking t…
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Hi - When I try to index multiple VCF files data/*.gz, it only takes the first VCF file for indexing and not all in the directory. Can it only take one input VCF file at a time?
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Change gene.iobio to show variants and depth (from alignments) for genes on alternate contigs.
For example, gene GSTT1 for build GRCh38 (RefSeq transcripts), the app is not able to display variants…
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Hi @starskyzheng
I’m using PanPop under a Conda environment to merge structural variant (SV) VCF files. These VCF files had previously been merged using bcftools as I’m working with multiple sampl…
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I am currently performing imputation on 23 chromosomes in vcf.gz files on my server. However, after imputation, I only obtained .vcf.gz files and did not get INFO.gz like others.
This is the comman…
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Ubuntu 18.04
htslib 1.15.1-19-g3c44c0b
"liftover" at 1.21-25-g9d314180
80 cpu
512GB RAM
I am attempting to liftover a VCF of ~5 million variants for a single sample. I have tried a BCF, and ind…
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Hi, I'm a Ph.D student in bioinformatics,
And I have some questions while using the "minigraph-cactus".
I run the program, in order to get some pangenome and vcf files in the graph.
I have 24 sequ…
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For many downstream analysis it would be nice to also publish the VCF files with the ref/alternate allele and the frequencies.
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Hello,
I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them usin…
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Hi. Jody, we still got update_db Crash. See attached file.
[log.txt](https://github.com/user-attachments/files/17229972/log.txt)