User: Helene
Helene • 390
- Reputation:
- 390
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- United States
- Last seen:
- 1 month ago
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- 3 years ago
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Posts by Helene
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... I had a little experience with VarScan2 - don't you need to use samtools pileup? I recall the pileup procedure to be painfully long too... Maybe I did not do it correctly, but please comment on it. Thank you. ...
written 5 weeks ago by
Helene • 390
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... I used Mutect2 on human exome sequencing (30x) data before and without parallel processing, it took me 5.5 days. That was still doable - However, now I am trying to run Mutect2 on my human WGS data (30x, bqsr bam file size ~120G), the estimation tells me 500+ weeks at the start!
I feel like even I ...
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... By the way, would you please comment on why the software did not take the line3 and line2 as one single indel case? ...
written 7 weeks ago by
Helene • 390
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... Thank you for the reply. By low allele freq, do you mean that the one of the allele is only supported by limited number of reads, but somehow the germline caller captured it? Of curiosity, have you done such comparison using your data? ...
written 7 weeks ago by
Helene • 390
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... Thank you so much for the reply. Great points! I added some adjacent lines from the original file, and interestingly all the "1" GT cases are next to a indel case. I wonder why IVC did not put line3 with line2 as an indel case... ...
written 7 weeks ago by
Helene • 390
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... I have a few cancer samples that were analyzed using GATK germline pipeline (call SNVs of each sample, not the cohort study setting). Recently we got the corresponding normal samples sequenced, and I did GATK on them as well.
I obtained one sets of somatic calls by subtracting the germline cancer ...
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... I recently got some VCF files from Illumina (IVC output), and I noticed that there are certain lines having GT field only with 1 number. For example, see the 3rd line below (I'm including the adjacent lines.):
chr1 21723729 . T C 123.0 PASS SNVSB=-17.2;SNVHPOL=4 ...
written 7 weeks ago by
Helene • 390
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... Hi @AlexReynolds Thank you so much for the reply and introducing bedops! I will give a short:) ...
written 9 weeks ago by
Helene • 390
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... I guess it is more of an algorithm question. I have a group of large bedgraph files (shown below, contains every single position of the genome), each is about 20-30Gb in size. I need to look into these files and locate the lines having locations match another file (small, < 100kb) (e.g. file test ...
written 10 weeks ago by
Helene • 390
• updated
9 weeks ago by
Alex Reynolds ♦ 20k
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... You are right about the line. I edited my answer. As for dictionary, I'm used to it to avoid any duplicated record in filtered.id file. That said, I guess even there are duplicated records, it does not matter in this case. Thank you for your reply. ...
written 10 weeks ago by
Helene • 390
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For Develop an R package for CRAN vs BioConductor
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created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
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For Remove both pair end reads with low mapping quality using Samtools
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For Remove both pair end reads with low mapping quality using Samtools
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For Non-cancer somatic mutation calling
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6 months ago,
created a question with more than 1,000 views.
For Remove both pair end reads with low mapping quality using Samtools
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For Develop an R package for CRAN vs BioConductor
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asked a question that was upvoted at least 5 times.
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For Non-cancer somatic mutation calling
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For Identify point mutations from each read in sam files
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