Moderator: finswimmer

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finswimmer13k
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Posts by finswimmer

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Comment: C: Extracting Allele Frequencies at a set of given positions
... Hello https://www.biostars.org/u/8531/, could you please show some example lines of your vcf and the expected output? Very likely [bcftools query](http://www.htslib.org/doc/bcftools.html#query) will help you with this task. fin swimmer ...
written 3 days ago by finswimmer13k
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Answer: A: Extract N amino acids from fasta file
... Using [seqkit](https://bioinf.shenwei.me/seqkit/usage/#subseq): $ seqkit subseq -r 1:30 input.fasta ...
written 3 days ago by finswimmer13k
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Comment: C: Switch ref/alt alleles vcf file
... Hello mdstep, if you have already a list of positions and REF/ALT alleles you want to switch, you could try something like this: 1. The list must be one of the support types by [bcftools annotate](http://www.htslib.org/doc/bcftools.html#annotate) and must contain an ID 2. Use this list and `bcftoo ...
written 7 days ago by finswimmer13k
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Answer: C: sorting a multi-sample (genotype) vcf file
... Hey, try this: $ bcftools query -l input.vcf | sort > samples.txt $ bcftools view -S samples.txt input.vcf > output.vcf If not already done, I would also suggest to use `bcf` instead of `vcf` or `vcf.gz`. This really improves speed when working with `bcftools` on large datasets. fi ...
written 10 days ago by finswimmer13k
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Comment: C: How to read fastq file with Python
... In this case `pysam` might be the right hammer ... :) ...
written 12 days ago by finswimmer13k
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Comment: C: bcftools variant filteration
... Hello, the `DP` value in the `INFO` is the sum of the DP value over all samples in your vcf at this position. The `DP` value in the `FORMAT` column in the read depth for the given sample at this position. If you just have one sample this value should be equal. You have to decide which one you need ...
written 12 days ago by finswimmer13k
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Comment: C: Error with bcftools and vcftools and removing individuals
... Hello, could you please show the header and one variant line? fin swimmer ...
written 18 days ago by finswimmer13k
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Answer: A: Does BQSR remove duplicate sequence in library?
... Hello https://www.biostars.org/u/45196/ , you are mixing things up. BQSR (Base Quality Score Recalibration) and MarkDuplicates are two different things. 1 BQSR (Base Quality Score Recalibration): The quality values assigned to each base within a read by sequencing machine gets reassigned by new v ...
written 21 days ago by finswimmer13k
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Comment: C: merge multiple files by commom column names
... The columns must be separated by whitespaces and not tabs. That's the only requirement. > I get a syntax error. When ever you receive any kind of error or something "doesn't work": Please give us the details! fin swimmer ...
written 25 days ago by finswimmer13k
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Comment: C: merge multiple files by commom column names
... The warning is just a warning. You can ignore it for now or do what it suggest. But there must be something strange with your input. I've tested it with the data you gave above and that's the output I get: id SNP2 SNP3 162 BB AA 172 BB AB 189 BB AA 1590 AB BB 182 BB AA ...
written 25 days ago by finswimmer13k

Latest awards to finswimmer

Popular Question 3 days ago, created a question with more than 1,000 views. For Converting MNP to SNP
Scholar 8 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Popular Question 9 days ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: Filter Fastq file by seq
Appreciated 21 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 22 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Appreciated 22 days ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
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
Popular Question 27 days ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Scholar 27 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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Scholar 29 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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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Teacher 9 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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Scholar 11 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file

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