User: Tootiki

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Tootiki0
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Posts by Tootiki

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Answer: A: how do i run pindel on a haploid genome
... spoke to pindel team and got this answer: > It looks like that we need to further work on the ploidy part and > re-work on pindel2vcf. For now, please consider 0/0 as 0, both the > other two as 1. ...
written 13 months ago by Tootiki0
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how do i run pindel on a haploid genome
... i'm trying to get pindel to call for a haploid genome, but it only seems to want to give me diploid results. my command is: pindel \ -f REF_GENOME.fasta \ -i LIST_OF_INPUT_BAMS.txt \ -c ALL \ -o OUTPUT_FILE \ -T 20 \ --Ploidy PLOIDY_INPUT_FILE.txt and the contents of P ...
genome sequence next-gen sequencing pindel written 13 months ago by Tootiki0
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Answer: A: filtering pindel results
... if anyone else is looking for the answer, i have it! firstly, to be clear, i'm always talking about the vcf file made by pindel2vcf from my initial pindel results file. this contains many sites that pindel doesn't predict as alt in any whole samples. ***i think*** that any site that is predict ...
written 13 months ago by Tootiki0
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filtering pindel results
... I have BAMs from which I am trying to detect reliable variants, to find differences between two strains of Aspergillus. I have used HaplotypeCaller to call call SNPs and small InDels, and Pindel to call longer InDels and other structural variants. I understand that filtering is always a balancing a ...
indel calling rearrangement filtering pindel written 15 months ago by Tootiki0

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