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### Subject of the issue
Question regarding String fields in VCFs/BCFs
Allele specific annotations fields such as AS_RAW_ReadPosRankSum are coded as Strings in VCFs. The header specifies the field a…
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It would be nice to have the ability to filter variants based on the alternate allele frequency in specific subsets of individuals. Currently, we can filter based on the counts of specific genotypes, …
arq5x updated
8 years ago
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Hi, I have a question about how reads are assigned as conflicting, unassignable etc.
I've been trying to use SNPsplit on noisy PacBio long reads to help with haplotype-resolved assembly (which I kn…
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I tried to run the snpfilter.sh to obtain the vcf file for uncovering the allele-specific copy number alternations in the tumor samples. I prepared tumor bam file, common dbSNP vcf file, and hg38.fa, …
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Hi!
Thank you for providing this tool.
I encountered a minor issue while using GLnexus and would like to seek your guidance.
Initially, I used GLnexus to merge five datasets, each consisting …
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> By the way, allele_specific_modification.py does something very similar to differential_modification.py, only focussing on a simpler case of a 1 vs 1 comparison. The same improvements can probably b…
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By screening though the code of the read_vcf() function of Fred2.IO.FIleReader I noticed the following:
_l194:_ v_list = record.ALT with record an item of vl being a Record object from pyvcf pa…
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Currently, figuring out what fields are available requires running a command like:
```
gsutil cat gs://gnomad-public/release/2.0.2/vcf/exomes/gnomad.exomes.r2.0.2.sites.vcf.bgz | gunzip -c - | head …
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Hello,
In large cohorts (~100K) multi-allelic sites are very common. Furthermore, good rare alleles can share the locus of bad, "common" variants (they are common since they seem to appear in many in…
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Dear group,
Thanks so much for developing such a great software. I met a specific issue during harmonising exposure and outcome.
In one SNP, the exposure and outcome share same effect allele, non-…