Moderator: finswimmer

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finswimmer13k
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Posts by finswimmer

<prev • 1,624 results • page 1 of 163 • next >
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Answer: A: Changing Sample Names in Merged VCF file
... Hello, [bcftools reaheder](http://www.htslib.org/doc/bcftools.html#reheader) should help you here. To use it, you have to prepare a text file, where in each line you write the old and the new sample name. Or just the new sample name, but all names in the order they should appear in the vcf. Then y ...
written 5 days ago by finswimmer13k
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Comment: C: Sort VCF File by Position?
... `bcftools sort` is absolute the right way and the way I would go today :) ...
written 8 days ago by finswimmer13k
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Comment: C: Slice multiple sequences with Biopython>SeqIO from fasta file - AttributeError:
... Hello https://www.biostars.org/u/39092/, this gives you a list of sequences: ``` domains = list(SeqIO.parse("domains.fa",'fasta')) ``` Later you try this ``` seq_n = domains.seq[0:num] ``` You have to define which element of the list you want to access, e.g. ``` seq_n = domains[0].seq[0:num] ` ...
written 9 days ago by finswimmer13k
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Comment: C: how to remove duplicate SNP rows in vcf using bcftools norm
... Hm, do you have an example of your vcf file? This works for me: ``` ##fileformat=VCFv4.2 ##contig= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 chr1 977330 rs2799066 T C 225 PASS . GT 0/1 chr1 977330 rs2799066 T C 225 PASS . GT 0/1 ``` ``` $ bcftools norm -D in.vcf ##fileformat=VCFv ...
written 11 days ago by finswimmer13k
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Answer: C: how to remove duplicate SNP rows in vcf using bcftools norm
... Shouldn't it be: ``` bcftools norm -D in.vcf -o out.vcf ``` (uppercase `D`) ? ...
written 11 days ago by finswimmer13k
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Comment: C: Fasta file not matching VCF
... Do you have insertions or deletions in your vcf? If so, then chr22:260034 in the consensus fasta will not represent the same position in the original fasta. ...
written 12 days ago by finswimmer13k
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Comment: C: freebayes VCF get average base quality of supporting bases of variant
... Hello https://www.biostars.org/u/41746/ , not an answer to your question, but why do you want to calculate the average base quality? fin swimmer ...
written 15 days ago by finswimmer13k
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Comment: C: bcftools view filter exclude not working when using logical operators
... Hello https://www.biostars.org/u/48569/ , could you please add an example of your vcf including the header an some variant lines? fin swimmer ...
written 22 days ago by finswimmer13k
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Comment: C: Break_blocks conversion of gvcf -> vcf
... Unless I've not missed an important point you can use `bcftools` to extract variant sites from a gvcfs $ bcftools view -m2 input.vcf The `-m` parameter filters for sites with a minimum number of alleles listed in REF and ALT. ...
written 28 days ago by finswimmer13k
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Comment: C: How to map the first part of a read and ignoring the rest of it?
... Is it of interest where the sequence align? Or is the question just "Do I have virus A and/or virus B" sequence in? For the later one [bbduk](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/) might be helpful. See the usage example about "Kmer filtering". ...
written 6 weeks ago by finswimmer13k

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Good Answer 12 days ago, created an answer that was upvoted at least 5 times. For A: what is the difference between polymorphism and mutation and variant?
Scholar 27 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 6 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 9 weeks ago, created a question with more than 1,000 views. For CollectHsMetrics Mean_Target_Coverage vs. mean_coverage in PER_TARGET_COVERAGE
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Converting MNP to SNP
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Good Answer 12 weeks ago, created an answer that was upvoted at least 5 times. For A: Filter Fastq file by seq
Appreciated 3 months ago, created a post with more than 5 votes. For A: Ensembl: Genes versus Transcripts
Scholar 3 months ago, created an answer that has been accepted. 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
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
Popular Question 3 months ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
Scholar 3 months ago, created an answer that has been accepted. 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
Scholar 3 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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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
Scholar 3 months ago, created an answer that has been accepted. 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
Popular Question 3 months ago, created a question with more than 1,000 views. For Counting soft clipped bases and reads
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

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