-
I have noticed the following behavior.
Suppose I have two files and a reference index:
```
echo -e "##fileformat=VCFv4.2\n##contig=\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\nchr1\t1\t.\tA\t…
-
Greetings,
I'm running into an error when chunking the reference. Here is my command
```
singularity exec /data/containers/glimpse_v2.0.0-27-g0919952_20221207.sif GLIMPSE2_split_reference \
--re…
-
Hi Simon,
Thanks again for your help earlier with the non-stranded issue. I am having one (hopefully easy-to-fix) issue with methylation extraction.
Running `extract` on a few human WGBS dataset…
-
@kike-garbo would it make sense to store additional bcf data like markups in Rhino.DocObjects.ViewportInfo objects? Or what would be the best way to get a persistence for userdata? Viewports themselve…
-
Hi! When running cue, I am getting an error:
```
[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tab
s: …
-
The `delly filter -f germline WI.DELLYpif.raw.bcf -o WI.DELLYpif.germline-filter.bcf` command in proc_genos process might be overly stringent on filtering SVs. Is this based on allele frequency? We …
-
If I attempt to add a header string to a VCF header using `bcf_hdr_append()`, the string gets passed to the function `bcf_hdr_parse_line()` which parses the key and passes it to `bcf_hrec_add_key()`. …
-
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 …
-
Hi
Can I ask how to solve this problem when i was running sort_vcf_same_as_bam.sh
[E::bcf_hdr_read] Input is not detected as bcf or vcf format
sort_vcf_same_as_bam.sh: line 146: 25158 Done(1)
-
As far as I can tell, there is currently no way to update genotypes in a bcf `Record`.
Related:
https://github.com/rust-bio/rust-htslib/blob/ed217c2fe460794d249e58a85db0b0c8a2929e55/src/bcf/record…