User: kulvait

gravatar for kulvait
kulvait250
Reputation:
250
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Czech Republic
Last seen:
3 years, 6 months ago
Joined:
5 years, 10 months ago
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Posts by kulvait

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Finding sample swaps using VCF files
... Yes, exactly. I want to check if the samples that are labeled by single person have very similar genetic profiles. ...
written 3.5 years ago by kulvait250
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Strip primer sequences from sequencing reads
... Hi, I have amplicon sequencing data from Illumina TrueSight Myeloid cancer panel. I have exact coordinates of each amplicon and primer sequences. And I have implemented Java code using htsjdk.samtools library to strip primer sequences from paired end mapped data. The idea is that if there are over ...
amplicon-seq dna-seq bam written 3.5 years ago by kulvait250 • updated 3.5 years ago by Robert Sicko630
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Finding sample swaps using VCF files
... Hi, I have bunch of samples from cancer patients amplicon sequencing. We are trying to identify somatic mutations related to those. I would like to perform check for sample swaps in these samples since we have typically more than one sample per patient. What comes into my mind is to produce VCF fil ...
vcf amplicon-seq dna-seq written 3.5 years ago by kulvait250
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Comment: C: Weird alignments in amplicon sequencing
... I have been using bwa mem with default parameters. This problem affects minority of the data. Thank you for recomendation, do you have experience with particular setting, we will consider using that. ...
written 4.3 years ago by kulvait250
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Comment: C: For bam and mutation signature I need coverage and number of observations
... Well, thank you I found the problem. There was files together with file.bam in directory file.bam file.bai file.bam.bai Index file file.bam.bai contained up to date index while the file.bai contained outdated index. I needed to remove incorrect file.bai and then the program works wit ...
written 4.3 years ago by kulvait250
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Comment: C: For bam and mutation signature I need coverage and number of observations
... Well, I have plenty of errors of the type ERROR: Read name 700834F:16:HAYDCADXX:1:1206:13536:58893, Mate not found for paired read Problem is that GATK tools did some kind of filtering and removed some reads without their mates. So I probably need to do that manually. Or is there some tool to ...
written 4.3 years ago by kulvait250
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Comment: A: For bam and mutation signature I need coverage and number of observations
... Thanks Pierre, at least for SNP detection this is a good solution. Unfortunately it does work only for my unprocessed bam files. After processing them further by picard/GATK there is error Nov 10, 2016 11:54:30 AM com.github.lindenb.jvarkit.tools.misc.FindAllCoverageAtPosition scan SEVERE: ...
written 4.3 years ago by kulvait250
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Comment: C: IndelRealigner and RealignerTargetCreator for amplicon sequencing
... Thank you, would it be then wise to just add all amplicon coordinates to interval file? ...
written 4.3 years ago by kulvait250
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Comment: C: IndelRealigner and RealignerTargetCreator for amplicon sequencing
... Thank you, it did the trick. ...
written 4.3 years ago by kulvait250
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IndelRealigner and RealignerTargetCreator for amplicon sequencing
... Hi, I am trying to incorporate indel realignment step to my processing pipeline. I use myeloidampliconpanel from Illumina that contains ~1000 amplicons and in total ~100Kb of genome coverage. Prior to the indel realignment step I clean my bams so that no reads are present outside of my amplicons. ...
indel amplicon-seq ngs written 4.3 years ago by kulvait250 • updated 4.3 years ago by WouterDeCoster45k

Latest awards to kulvait

Popular Question 4.3 years ago, created a question with more than 1,000 views. For Filtering bam files generated by bwa mem
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Variant caller for low frequency variants
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Determine sex from vcf file (or sequencing data)
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Determine sex from vcf file (or sequencing data)
Scholar 4.8 years ago, created an answer that has been accepted. For A: Determine sex from vcf file (or sequencing data)
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Determine sex from vcf file (or sequencing data)

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