User: gab

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gab20
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Posts by gab

<prev • 14 results • page 1 of 2 • next >
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Comment: C: different bam from same NGS data
... Yes, same exact file fasta ...
written 8 months ago by gab20
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Comment: C: different bam from same NGS data
... I guess so, although I'm still waiting for the guy who did the first analysis to reply ...
written 8 months ago by gab20
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different bam from same NGS data
... I was given some bam files I used to call somatic variants. The high number of SNP and mutations i found seemed suspicious, so I asked for the original fastq files to redo the allignment. While waiting for them I tried to get fastq from those bam files using `bedtools bamtofastq` . I used bwa mem to ...
bam bwa written 8 months ago by gab20 • updated 8 months ago by jsporter60
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Answer: A: samtools mpileup keeps making an empty file
... Try to pass `-f ` as a parameter before the bam files ...
written 8 months ago by gab20
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Comment: C: coverage of a SNP site?
... Can you specify the context? ...
written 10 months ago by gab20
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Answer: A: CNV analysis from vcf file
... To get data about CNVs you need usually .bam files which are essentially alligned FASTA foramet reads. So if you only have FASTQs you'll have to allign them. I used [cnvkit][1] to get the results, it has a very good user manual and it is still mantained. However to complete the analysis properly yo ...
written 10 months ago by gab20
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Comment: C: Calling somatic variants with Varscan
... vcf format is available as output, if the right option is given. I usaed the second of the workflows you mentioned, and it worked pretty well. ...
written 11 months ago by gab20
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Answer: A: CNV calling from exome sequencing data with a low number of samples
... I used [cnvkit][1] for this purpose. It does the job for one sample only at the time, if you have pairs of control-abnormal samples. You'll need many samples only if you do not have a control sample, and you want to build a reference as solid as possible. [1]: https://cnvkit.readthedocs.io/en/s ...
written 11 months ago by gab20
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Comment: C: Whole Exome Sequencing Depth
... Sequencing depth per se is not a key parameter, what is really important is the difference in read depth between normal and tumor samples, so you really should have both. A minimum value of depth is set to avoid false positives/negatives during calculations, usually it is a default parameter in to ...
written 11 months ago by gab20
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cnvkit flasso interrupt
... Hi I'm using cnvkit to get CNVs from WES data. I got my .cnr right and also the .cns files with all segmentation methods except for flasso which gives me the following output: Dropped 1 outlier bins: chromosome start end gene log2 depth weight 0 ...
exome cnvkit written 12 months ago by gab20

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