Moderator: finswimmer

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finswimmer11k
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Germany
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2 years, 3 months ago
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Posts by finswimmer

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Comment: C: Removing homozygous reference genotypes from multi-sample vcf file
... For me this does not sound surprisingly. If you have no sample within 1200 samples, which is hom REF on a given position, this means, that what is called ref, is very rare. Of course this is possible, but I would guess it is rare. ...
written 13 hours ago by finswimmer11k
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Comment: C: Removing homozygous reference genotypes from multi-sample vcf file
... Hmm, yes might be. In this case: bcftools view -e 'GT[*]="RR"' input.vcf ...
written 14 hours ago by finswimmer11k
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Answer: A: Removing homozygous reference genotypes from multi-sample vcf file
... I strongly recommend using existing tools for filtering vcf files. With bcftools it works like this: bcftools view -i 'GT[*]="alt"' input.vcf This will give you any site where at least one sample has an alternate allel. ...
written 15 hours ago by finswimmer11k
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Comment: C: -C 50 parameter MPILEUP
... Hello, using this parameter `bcftools` penalize read with lot of mismatches harder than most aligner will do, which greatly improve specificity in variant calling. The thought behind this, is to say the more mismatches in one read exists the higher the probability that the origin of this read is in ...
written 1 day ago by finswimmer11k
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Comment: C: Custom filteration of fastq file
... > Remove reads with unique sequence having read count less than 10. Could you please explain why do you want to do this? ...
written 1 day ago by finswimmer11k
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Comment: C: Error in SAM to BAM conversion
... Hello , ./bowtie2 -p 5 -x /ref/grch38 --no-unal -U fastq/SRR7541164.fastq > -S /fastq/test.sam Just a typo here or do you realy redirecte bowtie output to `-S`? What's the output of `tail /fastq/test.sam`? fin swimmer ...
written 2 days ago by finswimmer11k
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Answer: C: snpEff: Fatal error reading file the input VCF files and stop runing
... > WARNING: Unkown IUB code for SNP '-' You have a `-` in the 4th column (ALT) which is not allowed. Missing values have to be `.` in the vcf file. Furthermore a chromosome `0` and a position `0` looks also quite strange (but should be allowed) ... ...
written 3 days ago by finswimmer11k
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Comment: C: No reads in IGV at the positions indicated by the bed file
... Have a look if IGV filter out any reads. Go to View->Preferences->Alignment Here the Mapping Quality Threshold and all point with "Filter" are the most interesting once. ...
written 5 days ago by finswimmer11k
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Answer: A: tabix to exclude chromosomes from vcf
... Hello, using the `--help` parameter or start bioinformatic applications without any option first is always a good idea. $ tabix Version: 1.9 Usage: tabix [OPTIONS] [FILE] [REGION [...]] Indexing Options: -0, --zero-based coordinates are zero-based -b, --b ...
written 5 days ago by finswimmer11k
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Comment: C: snpEff for bacteria genome
... Hello, what's the name of your bacteria? How does your `snpEff.config` looks like? Is `database` just a placeholder here? fin swimmer ...
written 5 days ago by finswimmer11k

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Teacher 9 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 18 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 25 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
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Popular Question 8 weeks ago, created a question with more than 1,000 views. For Which human reference genome should I use?
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 12 weeks ago, created an answer that has been accepted. 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 3 months ago, created an answer with at least 3 up-votes. 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: Filter Fastq file by seq
Commentator 3 months ago, created a comment with at least 3 up-votes. For A: sam file error
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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
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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
Appreciated 3 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
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
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
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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

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