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Hi,
Thanks for the nice tool. I've been working ROH prediction using BCFtools for the WGS VCF. and got one question. Some predicted regions seems to be split by small chunks, and the region between…
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I noticed manta output records such as
# CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA20761
1 83829 MantaDEL:97931:0:0:0:0:0 GAGAAAGAAAGAAAGAAAGAAAGAA …
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ANGSD suite is very useful and relevant to study SNPs variation in low-coverage data and I am wondering about how to best take advantage of the existing framework to also study other kinds of variants…
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Hi
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HaplotypeCaller expends massive effort to generate a set of local candidate haplotypes along with their read likelihoods. After that, however, it throws away the haplotypes, using them _only_ for the…
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**1. What were you trying to do?**
I want to do the variant calling. and my code was "vg call ../Amana_graph.xg -r ../Amana_graph.snarls -k DLS01.pack -s DLS01 > DLS01.vcf".
**2. What did you …
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Should we add support ploidy number over 2 to bcftools call?
There are 4 or ploidy in some plant, so we need this feature.
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I'm running into an issue with:
> (phyluce) bash-4.2$ phyluce_snp_convert_vcf_to_structure --input filtered_unlinked.recode.vcf --output filtered_unlinked_structure.str
> Working.Traceback (most …
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I have observed inconsistency in genotype calling within a VCF file. Although most genotyping make sense with AO/RO number, but I found many instances where an individual with similar numbers of RO an…
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Hello, I have vcf files generated from bcftools convert --gvcf2vcf and this raises an issue
```
bedtools coverage -a A_vaga.NDPD.bed -b ARC_ancestor.expanded.g.vcf.gz -counts …
ghost updated
4 years ago