User: jamessemaj712

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Posts by jamessemaj712

<prev • 18 results • page 1 of 2 • next >
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Comment: C: connsensus file too big to read
... How can I locate the snp in such a big consensus file.I even don't know if there exists a snp? ...
written 19 months ago by jamessemaj71210
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connsensus file too big to read
... Hi, I am trying to use soapsnp.Ion chromosme 22 oh human38.I did all the steps for generating the consensus filr using soap snp to find if there are any snps in the consensus file.The problem is my consensus file is 2.7GB in size which is not opening in computer i.e. my laptop hangs and also it is ...
consensus soap snp variants written 19 months ago by jamessemaj71210
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Comment: C: vcf files in gatk not showing data lines
... where do I get to known sites parameter.I can't find it. ...
written 19 months ago by jamessemaj71210
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Comment: C: vcf files in gatk not showing data lines
... I have added the stack trace in 2 replies due to limit placed on the number of characters in the reply text area. ...
written 19 months ago by jamessemaj71210
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Comment: C: vcf files in gatk not showing data lines
... ``` INFO 10:46:36,135 ProgressMeter - Total runtime 209.68 secs, 3.49 min, 0.06 hours INFO 10:46:36,135 MicroScheduler - 169827 reads were filtered out during the traversal out of approximately 962428 total reads (17.65%) INFO 10:46:36,135 MicroScheduler - -> 0 reads (0.00% of total) faili ...
written 19 months ago by jamessemaj71210 • updated 18 months ago by Ram12k
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Comment: C: vcf files in gatk not showing data lines
... ``` INFO 10:43:04,724 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:43:04,734 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56 INFO 10:43:04,734 HelpFormatter - Copyright (c) 2010 The Broa ...
written 19 months ago by jamessemaj71210 • updated 18 months ago by Ram12k
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vcf files in gatk not showing data lines
... Hi, I tried using Gatk tool to find variants in a chromosome 21 of human genome. I used HaplotypeCaller tool for finding the variants using the following command: java -jar GenomeAnalysisTK.jar -R chr21/chr21.fa -T HaplotypeCaller -I chr21/alignments/human38chr21.sorted.bam -o chr21/variants/ans ...
haplotypecaller gatk indel snp written 19 months ago by jamessemaj71210 • updated 18 months ago by Biostar ♦♦ 20
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Dataset for NGS
... Hi, I am doing a project in which I intend to compare the tools for finding snp,indel and cnv.I tried many tools and was successful in running few of them.The problem now is that I want datasets that I can run so that I will surely find indel,snp or cnvs for instance.As I have limited hardware like ...
indel dataset snp cnv written 19 months ago by jamessemaj71210 • updated 19 months ago by rbagnall1.1k
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Problem in using Dindel
... Hi, I installed dindel and tried running the commands as follows.I am using the following manual for reference: https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxrZWVzYWxiZXJzfGd4OjQwZmM1ZTEzOWVjMzc5NDY The command I used is: ./dindel-1.01-linux-64bit --analysis getCIGA ...
indel sv dindel written 20 months ago by jamessemaj71210
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Comment: C: Problem using Breakdancer
... I dont know how to use perl.I want to use c++ version,but where to get it explicitly without requiring to interfere with perl.I mean can you provide me the link explicitly for c++ version and explanation to running it. ...
written 20 months ago by jamessemaj71210

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