Moderator: finswimmer

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finswimmer7.7k
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Posts by finswimmer

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Comment: C: Merge vcf files with multiple samples into one vcf with all variants
... Could you please post the complete header of the original vcf file and the first few variants? Thanks. fin swimmer ...
written 5 hours ago by finswimmer7.7k
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Answer: A: I16 Info Tag
... Hello https://www.biostars.org/u/50213/ , the output you are talking about, is the output of `bcftools mpileup`. And this is just the half way down the road to your variants. In this step `bcftools` collects metrics about each covered position on which `bcftools call` will decide if it should have ...
written 5 hours ago by finswimmer7.7k
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Comment: C: Failure in alignment with BWA using fusion reference genome
... - Can you index and align against `` only? - Can you index and align against `` only? - What's the output of `grep "chrV" -A 5 -B 5 `? ...
written 5 hours ago by finswimmer7.7k
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Comment: C: bcftools mpileup no output (empty calls.bcf file)
... Hello, you have to make sure that the `bam` files are coordinate sorted before doing variant calling. At least the first sample isn't. fin swimmer ...
written 1 day ago by finswimmer7.7k
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Comment: C: bcftools mpileup no output (empty calls.bcf file)
... How did you produce your bam file? Please show us the exact command used. ...
written 2 days ago by finswimmer7.7k
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Comment: C: bcftools mpileup no output (empty calls.bcf file)
... Hello and welcome to biostars https://www.biostars.org/u/50889/ , Please use the formatting bar (especially the `code` option) to present your post better. I've done it for you this time. Thank you. Are you sure that you will have any variants in your `aligned.bam`? > When I look at calls.b ...
written 2 days ago by finswimmer7.7k
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Comment: C: Merge vcf files with multiple samples into one vcf with all variants
... > But since the file I am using is not a standard VCF file, I am not getting the desired output. Could you please tell us, what makes your vcf a non standard vcf file? fin swimmer ...
written 2 days ago by finswimmer7.7k
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Comment: C: Failure in alignment with BWA using fusion reference genome
... Could you please try to reindex `fusion38-10k.fa`. But this time without any parameters. For -a bwtsw` you used I see a warning in the manual about it: Warning: `-a bwtsw' does not work for short genomes, while `-a is' and `-a div' do not work not for long genomes. Without sett ...
written 2 days ago by finswimmer7.7k
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Comment: C: Failure in alignment with BWA using fusion reference genome
... Let's check if the line ending terminators are correct. $ file : ASCII text If the output is `: ASCII text, with CRLF line terminators` you should install `dos2unix` and run `dos2unix `. fin swimmer ...
written 3 days ago by finswimmer7.7k
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Comment: C: pybedtools intersect using additional options
... I guess it must be : a.intersect(b, '-wb') Take care of the quotation marks, otherwise python interpret `wb` as a variable. fin swimmer ...
written 3 days ago by finswimmer7.7k

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Librarian 4 days ago, created a post with more than 10 bookmarks. For Creating workflows with snakemake and conda
Teacher 4 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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Teacher 5 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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