Moderator: finswimmer
finswimmer ♦ 13k
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Posts by finswimmer
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... Hello,
Biopython is unable to read the QUAL values from the abi header. I'm not sure if your file is somehow broken.
However, biopython doesn't catch this case correct. In the corresponding lines of code, they reference to `qual` and `seq` even if they might not assigned in the code before:
https ...
written 6 weeks ago by
finswimmer ♦ 13k
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Comment:
C: Exome data analysis
... Hello https://www.biostars.org/u/51501/,
the information you are giving are to general to give you concrete advice. How does your "txt" file looks like? (A vcf file would be much better.) What information are already in the file?
fin swimmer ...
written 10 weeks ago by
finswimmer ♦ 13k
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... If you like to use python, have a look at [pysam](https://pysam.readthedocs.io/en/latest/usage.html#working-with-vcf-bcf-formatted-files), which is a wrapper around the htslib C-API. ...
written 4 months ago by
finswimmer ♦ 13k
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... > But when i put in vep this mutation c.164+3083C>G(intron 2) into this format CFTR:c.164+3083C>G. how should i ensure correct annotation
If you have luck (and in most of the cases you will) you will only get one position and then you can be sure. Otherwise it is absolutely necessary to kn ...
written 4 months ago by
finswimmer ♦ 13k
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... Hello again,
in [ensembl's vep ](https://www.ensembl.org/Homo_sapiens/Tools/VEP) you can create a new job. In the "Input Data" section, you can write your gene of interest and the hgvs description, in your case: `CFTR:c.164+3083C>G`. Click "Run" and wait. Once the job is finished, click "View Re ...
written 4 months ago by
finswimmer ♦ 13k
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... Hello,
you have to find out the genomic location of the variant. Than you can use this position to search in gnomad.
You can find the position using [ensembl's vep](https://www.ensembl.org/Homo_sapiens/Tools/VEP) (7:117507446). You search will guide you to [this result](https://gnomad.broadinstitu ...
written 4 months ago by
finswimmer ♦ 13k
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Comment:
C: Merge vcf files with bcftools
... The reason for the issue in the linked post, was that there were variants which has no value for a specific info tag. So in your case look for variants which have a info tag `VAK_ug_AS_MQ` without a value. If this is the case you have the same issue.
The solution to for the issue is then to replac ...
written 5 months ago by
finswimmer ♦ 13k
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Comment:
C: Merge vcf files with bcftools
... Hello,
this one looks similar. Does it help?
* https://www.biostars.org/p/356438/
fin swimmer ...
written 5 months ago by
finswimmer ♦ 13k
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... Hello https://www.biostars.org/u/49398/,
`samtools view` returns all reads that overlap a given region. So it's expected to have information about the region outside you give.
You can use the `-r` parameter for `samtools depth` (or `-b` if you provide a bed file with regions) to get the coverage i ...
written 5 months ago by
finswimmer ♦ 13k
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... Hello,
[bcftools filter][1] with the `-s` argument is what you are looking for.
```
bcftools filter -e 'ID=@rsid.txt' -s 'MyFilter' input.vcf
```
fin swimmer
[1]: http://www.htslib.org/doc/bcftools.html#filter ...
written 5 months ago by
finswimmer ♦ 13k
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