Moderator: finswimmer
finswimmer ♦ 13k
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Posts by finswimmer
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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 6 days 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 8 days 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 10 days 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 10 days 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 4 weeks 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 weeks 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 6 weeks 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 6 weeks ago by
finswimmer ♦ 13k
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... GATK and bcftools use different quality markers and different thresholds for them, to determine which read they take into account for variant calling and which they skip. So a difference is normal. But in your case, that's looking to different to me.
Could you please provide the commands you've use ...
written 6 weeks ago by
finswimmer ♦ 13k
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... Hello https://www.biostars.org/u/65570/ ,
the problem occurs due to a malformed/strange bam file. How was this created?
fin swimmer
...
written 10 weeks ago by
finswimmer ♦ 13k
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