Moderator: finswimmer

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finswimmer13k
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Posts by finswimmer

<prev • 1,638 results • page 1 of 164 • next >
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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 6 days 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 8 days 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 10 days 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 10 days 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 4 weeks 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 weeks 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 6 weeks 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 6 weeks ago by finswimmer13k
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Comment: C: why GATK and BCFTOOLS output different number of DP
... 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 finswimmer13k
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Comment: C: GATK4 HaplotypeCaller - read is malformed
... 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 finswimmer13k

Latest awards to finswimmer

Teacher 6 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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Popular Question 17 days ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Student 23 days ago, asked a question with at least 3 up-votes. For Difference between | and || in filtering expressions by bcftools
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 27 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Merging FASTA files
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
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Scholar 3 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 3 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 3 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: what is the difference between polymorphism and mutation and variant?
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Popular Question 5 months ago, created a question with more than 1,000 views. For CollectHsMetrics Mean_Target_Coverage vs. mean_coverage in PER_TARGET_COVERAGE
Popular Question 5 months ago, created a question with more than 1,000 views. For Converting MNP to SNP
Scholar 5 months ago, created an answer that has been accepted. 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 6 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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