User: RobertUt

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RobertUt0
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Posts by RobertUt

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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 2 days ago by RobertUt0
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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 2 days ago by RobertUt0
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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 2 days ago by RobertUt0

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