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Hi,
I'm running Delly version 8.5 in Centos for detecting Germline SVs from novaSeq Short reads. So I have few doubts arisen while using Delly.
1. While running GermlineSV calling for a single sam…
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Hi
I'm trying to run phase_common_static on my cow array data, and blocked with this error:
phase_common_static --region 1 -I huellas.vcf.gz -O huellas_prueba.bcf --log log.txt -T 8
[SHAPEIT5] p…
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I have a vcf file and i wanted to drop the chroM variants which i was unable to do with the bcftools view input.vcf.gz --regions chr1 it gives the error " could not load the index.
and when i follow…
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Rather, there should be a mut and non-mut `Info` type similar to how there is `iter()` and `iter_mut()`.
@johanneskoester what do you think?
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In the documentation it says under ```bcf::record::Record::push_info_float```
_**Add**/replace a float-typed INFO entry._
However when trying to add an INFO field from another VCF file I get th…
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Hey there,
I'm noticing when using make-gnotate with multiple gnomad vcf.gz files which you described as such:
```
slivar make-gnotate --prefix gnomad-2.1 \
--field controls_nhomalt:gnoma…
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Here is what I am running:
```
samtools mpileup -t DP,DV,DP4,SP -g -f ../reference/ce10/ce10.fa -r chrI JU2464.bam | bcftools call -T ../individual_bcf/complete_variant_set.bcf --format-fields GQ,GP …
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I'm having an issue supplying allele frequencies as answered in #28. Unfortunately I can't provide example data, but I'll try to provide as much as I can without supplying sensitive data.
### backg…
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### Description of the bug
Hi,
I had the following error, which stems from an empty `smoove.vcf.gz` input file. I'm not entirely sure but I believe the reason why this file is empty is because s…
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Hello,
I am using popscle dsc-pileup function as a prelude for running demuxlet on cellranger output. Here is my code:
`packages/popscle/bin/popscle dsc-pileup --sam bam.bam --vcf vcf1.vcf --out h…