Moderator: finswimmer

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finswimmer13k
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Posts by finswimmer

<prev • 1,640 results • page 1 of 164 • next >
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Comment: C: SeqIO error: local variable 'qual' referenced before assignment
... 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 finswimmer13k
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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 finswimmer13k
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Comment: C: Doing an operation on one huge VCF, use Python or would C be faster (somewhat ni
... 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 finswimmer13k
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Comment: C: gnoMAD specific mutation allele position in gnoMAD
... > 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 finswimmer13k
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Comment: C: gnoMAD specific mutation allele position in gnoMAD
... 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 finswimmer13k
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Answer: A: gnoMAD specific mutation allele position in gnoMAD
... 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 finswimmer13k
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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 finswimmer13k
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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 finswimmer13k
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Answer: A: Why Samtools view don't extract sequence out of the given region?
... 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 finswimmer13k
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Answer: A: Soft filtering of SNPs in a list
... 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 finswimmer13k

Latest awards to finswimmer

Teacher 22 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 26 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Epic Question 8 weeks ago, created a question with more than 10,000 views. For Creating workflows with snakemake and conda
Great Question 8 weeks ago, created a question with more than 5,000 views. For Which human reference genome should I use?
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: Extract SNPs from VCFfile located in genes based on GFF file information
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Which human reference genome should I use?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Extract SNPs from VCFfile located in genes based on GFF file information
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 3 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 4 months ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Student 4 months ago, asked a question with at least 3 up-votes. For Difference between | and || in filtering expressions by bcftools
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 5 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Merging FASTA files
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 5 months ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 7 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 7 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 7 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file

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