Forum: Bioinformatics
04-02-2015, 07:17 AM
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Replies: 7
Views: 7,664
No I have already figured out a tool that works...
No I have already figured out a tool that works best for this.. the bedops tool has a function vcf2bed works fit to convert the scenario and I already performed that and also am familiar with awk as...
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Forum: Bioinformatics
04-01-2015, 07:46 AM
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Replies: 7
Views: 7,664
@inesdesantiago
I have a situation where I have...
@inesdesantiago
I have a situation where I have output of SNPs from VarScan. I see the varscan outputs LOH( both as SNP and INDELS LOH). Now for INDELS its fairly easy to make a bed format file. But...
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Forum: Bioinformatics
03-26-2015, 08:01 AM
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Replies: 10
Views: 21,029
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Forum: Bioinformatics
03-25-2015, 11:43 AM
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Replies: 10
Views: 21,029
I would just want to ask you in case you have...
I would just want to ask you in case you have have not other bases as 0 in normal in that case do you still calculate the variant allele frequency as the above? Variant allele frequency should be...
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Forum: Bioinformatics
03-09-2015, 04:34 AM
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Replies: 0
Views: 1,471
Problem with Pindel output
Hi,
I have been using normal/tumor GATK processed realigned and recalibrate bam files for mutation , indel and CNV analysis. I have used this bam with VarScan, GATK, Lofreq, Mutect and I have...
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Forum: Bioinformatics
02-09-2015, 05:53 AM
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Replies: 0
Views: 1,373
Using Phylosub for Inferring clonality
Hi,
I have recently come across a paper which developed a software phylosub with which one can infer the clonal heterogenity in both single sample tumors or more samples. I have WES data of ...
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Forum: Literature Watch
02-05-2015, 02:34 AM
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Replies: 77
Views: 52,777
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Forum: Bioinformatics
01-27-2015, 06:45 AM
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Replies: 3
Views: 2,031
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Forum: Bioinformatics
01-27-2015, 06:16 AM
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Replies: 11
Views: 5,483
am using the GATK DepthofCoverage output for...
am using the GATK DepthofCoverage output for exomeCNV, but am getting some error in dataframe.
My commands for normal and tumor for 3 chromosomes
chr.list = c("chr19","chr20","chr21")
normal =...
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Forum: Bioinformatics
01-27-2015, 03:13 AM
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Replies: 3
Views: 2,031
@mrfox
Did you find a workaround for this? I...
@mrfox
Did you find a workaround for this? I am also facing issues, am using ExomeCNV for first time, the bamcoverage.sh does not work well as they need old version of samtools, so I tried gatk...
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Forum: Bioinformatics
01-26-2015, 09:48 AM
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Replies: 11
Views: 5,483
@spoonman
I would like to know how to make...
@spoonman
I would like to know how to make the files read if I take the output of GATK depthofcoverage, since it contains one file that contains all the chromosome summary together. How do I use...
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Forum: Bioinformatics
11-19-2014, 02:41 AM
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Replies: 4
Views: 4,045
Filtering varscan variants
I would like to ask removing the snps closer to indels at 1bp thus removes a lot of snps for me. But it is not a test for false positive right? I believe if am using the local realignment around...
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Forum: Bioinformatics
11-18-2014, 06:28 AM
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Replies: 2
Views: 1,932
I also have a same question,
I have also ran...
I also have a same question,
I have also ran the VarScan2 on my normal/tumor pair with p-value as 0.1 somatic p-value 0.001 and then ran the somatic filter with parameters -min-strands2 2...
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Forum: Bioinformatics
09-03-2014, 05:18 AM
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Replies: 10
Views: 21,029
@lethalfang
`Would you like to share the...
@lethalfang
`Would you like to share the pipeline for finding somatic mutations. I have 2 samples, one low and one high grade tumor and its normal. I want to detect the point somatic mutations. I...
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Forum: Literature Watch
07-14-2014, 04:48 AM
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Replies: 77
Views: 52,777
Dear Velntina,
Please find the output for...
Dear Velntina,
Please find the output for the above call, I have made 6 such calls but all had the same problem. Below am attaching the log of the output run and at what stage I get the...
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Forum: Literature Watch
07-14-2014, 03:37 AM
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Replies: 77
Views: 52,777
Hi ,
I am using control-FREEC with exome...
Hi ,
I am using control-FREEC with exome sequencing data, so far I have been successful in implementing it on my normal control tumor pairs for CNA detection. I am now curious to apply it further...
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Forum: Bioinformatics
10-18-2013, 03:32 AM
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Replies: 9
Views: 20,562
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Forum: Bioinformatics
10-18-2013, 02:55 AM
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Replies: 9
Views: 20,562
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Forum: Bioinformatics
10-09-2013, 04:34 AM
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Replies: 18
Views: 15,899
@choishingwan
I guess then I can use the...
@choishingwan
I guess then I can use the option of TableRecalibration, I am yet to run it , if it produces a bam file good enough else I will use the print read option which will surely produce a...
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Forum: Bioinformatics
10-09-2013, 03:40 AM
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Replies: 18
Views: 15,899
@choishingwan ,
Thanks for your prompt...
@choishingwan ,
Thanks for your prompt reply. I would like to tell you that I am using the version 2.3 not the 2.7 one so is it wrong to use the DBSNP_137.vcf file with that? I hope this should...
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Forum: Bioinformatics
10-09-2013, 03:31 AM
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Replies: 18
Views: 15,899
@thedamain,
I need some information about...
@thedamain,
I need some information about the exomes.bed file which you are using. I see that most of the pipelines say that they generate it from the UCSC genome browser to restrict the output...
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Forum: Bioinformatics
10-09-2013, 03:02 AM
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Replies: 18
Views: 15,899
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Forum: Bioinformatics
10-09-2013, 02:59 AM
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Replies: 18
Views: 15,899
@thedamian,
Yes I fixed it , I indexed it...
@thedamian,
Yes I fixed it , I indexed it again and then made the call and the local realignment step is running now. But i need some inputs for the base quality recalibration step. In the above...
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Forum: Bioinformatics
10-09-2013, 01:47 AM
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Replies: 18
Views: 15,899
Hi I am facing some problems with the Local...
Hi I am facing some problems with the Local realignment step around the indels, I am using the marked bam file after the PCR duplicate marking step but I am getting the following error
##### ERROR...
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Forum: Bioinformatics
10-07-2013, 12:47 PM
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Replies: 18
Views: 15,899
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