User: Helene

gravatar for Helene
Helene390
Reputation:
390
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Trusted
Location:
United States
Last seen:
2 weeks, 4 days ago
Joined:
3 years, 2 months ago
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Posts by Helene

<prev • 96 results • page 1 of 10 • next >
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Comment: C: Locate positions in a large bed file
... Thank you very much for the detailed information. The list of positions I'm talking about is no longer at reads level - they are just chromosome & positions. It looks like I should turn this list into another bed file, and just use "6.1.2.3.3. Retrieving elements which overlap target elements" a ...
written 5 weeks ago by Helene390
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Comment: C: Locate positions in a large bed file
... Thank you so much for your reply. I am looking at this too - do you happen to know how fast these two functions are for large files? ...
written 5 weeks ago by Helene390
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Locate positions in a large bed file
... I have a ~20G bed file for a few samples, and the bed file contains read depth for all positions of the human genome. Also, I have a list of chromosome positions (~30,000 to 50,000) for each sample, and I would like to know the read depth at these positions. What would be the most efficient method p ...
bed written 5 weeks ago by Helene390 • updated 5 weeks ago by Alex Reynolds21k
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Comment: C: Mutect 2 on WGS data takes too long to run
... 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 3 months ago by Helene390
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Mutect 2 on WGS data takes too long to run
... 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 ...
wgs mutect written 3 months ago by Helene390 • updated 3 months ago by donfreed1.1k
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Comment: C: GT field in VCF only has one number?
... By the way, would you please comment on why the software did not take the line3 and line2 as one single indel case? ...
written 3 months ago by Helene390
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Comment: C: somatic calls by somatic SNV caller differ a lot, when comparing with cancer min
... 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 3 months ago by Helene390
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Comment: C: GT field in VCF only has one number?
... 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 3 months ago by Helene390
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somatic calls by somatic SNV caller differ a lot, when comparing with cancer minors normal germline calls
... 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 ...
somatic snv snp written 3 months ago by Helene390 • updated 3 months ago by d-cameron880
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GT field in VCF only has one number?
... 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 ...
vcf written 3 months ago by Helene390

Latest awards to Helene

Popular Question 3 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 3 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 3 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 3 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Popular Question 4 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 8 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 8 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 9 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 10 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 11 months ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
Student 12 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Student 18 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Scholar 18 months ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Illumina's HiSeq strange Phred quality score
Scholar 20 months ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Supporter 20 months ago, voted at least 25 times.
Scholar 21 months ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

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