User: RobertUt

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RobertUt10
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7 months ago
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7 months, 2 weeks ago
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r*******@students.uu.nl

Posts by RobertUt

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Comment: C: The fasta sequence does not match the REF allele at chr1:1298836 ?
... Hi fin, might be a curious question: What do you normalize your `vcf file` for? Because I don't see how normalizing would have helped to solve my problem. Ut ...
written 7 months ago by RobertUt10
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Answer: A: The fasta sequence does not match the REF allele at chr1:1298836 ?
... Problem solved: The problem seems to occur whenever an indel is overlapping a SNP. `Bcftools` apparently replaces the `REF` C (1st line) by the `ALT` G, and cannot find the C in `REF` when trying to integrate the indel CAG (2nd line) into the reference. In our dataset there is only indels overlapp ...
written 7 months ago by RobertUt10
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The fasta sequence does not match the REF allele at chr1:1298836 ?
... Dear all, I am making a `consensus.fa` from a `aligned.bam` using `bcftools consensus`. cat reference.fa | bcftools consensus calls.vcf.gz > consensus.fa The generated `consensus.fa` only contains parts of chr1 and I get the following error: The site chr1:724953 overlaps with anot ...
vcf consensus bcftools written 7 months ago by RobertUt10
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Answer: A: bcftools mpileup no output (empty calls.bcf file)
... We finally found the solution: The downloaded `bam` was generated by paired end sequencing. For some unknown reason `bcftools` considers these read pairs to be "anomalous". By using the `-A` input option one prevents `bcftools` from skipping anomalous read pairs. Now it's working as it is supposed t ...
written 7 months ago by RobertUt10
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Comment: C: bcftools mpileup no output (empty calls.bcf file)
... Hi fin, the bam file I'm using is coordinate sorted. Robert ...
written 7 months ago by RobertUt10
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Comment: C: bcftools mpileup no output (empty calls.bcf file)
... The bam file wasn't generated in our on lab but was downloaded from: https://www.ebi.ac.uk/ena/data/view/PRJEB3371 It's a whole genome sequencing file, generated with Illumina HiSeq 2000. I am also suspecting the bam file to be the problem, because the fasta worked fine in previous commands. Chro ...
written 7 months ago by RobertUt10
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Comment: A: bcftools mpileup no output (empty calls.bcf file)
... Dear fin, Thank's for your suggestions. I just checked the bam file with samtools tview and found plenty of **variants**. By the way, the only warning/error I get is about ploidy and a chromosome, which is missing in my bam file but present in the reference fasta. Any other suggestions? ...
written 7 months ago by RobertUt10
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bcftools mpileup no output (empty calls.bcf file)
... Hi everyone, I am trying to make a consensus from a aligned bam file. This is my workflow: bcftools mpileup -Ou -f reference_HG19.fa aligned.bam | bcftools call -mv -Ob -o calls.bcf bcftools index calls.bcf cat reference_HG19.fa | bcftools consensus calls.bcf > consensus.f ...
consensus bcftools samtools mpileup calls.bcf written 7 months ago by RobertUt10

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Scholar 7 months ago, created an answer that has been accepted. For A: bcftools mpileup no output (empty calls.bcf file)

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