User: Jokhe

gravatar for Jokhe
Jokhe120
Reputation:
120
Status:
New User
Location:
Sweden
Last seen:
2 years, 11 months ago
Joined:
4 years, 5 months ago
Email:
j***********@uef.fi

Posts by Jokhe

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Use of if-else statement in snakemake rule
... Thank you Matt! Works like a charm! ...
written 3.5 years ago by Jokhe120
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Use of if-else statement in snakemake rule
... Hi! I'm building snakemake pipeline for `VarScan2` variant calling. As a result of `VarScan2`, I have six VCF files that must be processed individually and `bam-readcount` tool is a part of this processing. The use of bam-readcount depend on the type of variant; if I have somatic variant calls I sh ...
if-else python snakemake written 3.5 years ago by Jokhe120 • updated 14 months ago by schroder.julia0
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Comment: C: Merging raw Illumina FASTQ files with snakemake
... Thanks Devon, it works like a charm! It was so easy solution that I didn't even think about it. ...
written 3.6 years ago by Jokhe120
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Merging raw Illumina FASTQ files with snakemake
... Hi, I have sequenced DNA samples with Illumina NextSeq which produces 8 FASTQ files per sample. As a part of my `snakemake` pipeline I would like to merge these files into two larger FASTQ files (forward/reverse) and continue working with these files. I have tried to figure out how this could be do ...
illumina paired-end reads snakemake written 3.6 years ago by Jokhe120
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How to export CNVkit results into PyClone?
... Hi, I have performed targeted amplicon sequencing for paired normal-tumor samples and recently identified both somatic mutations (VarScan2 somatic) and copynumber changes (CNVkit's batch command) in my samples. I would like to move on and study the tumour heterogeneity within my samples with PyClon ...
cnvkit pyclone written 3.9 years ago by Jokhe120 • updated 3.9 years ago by Eric T.2.6k
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Comment: C: CNA clonality for non-WES/WGS data
... Thank you! I tried to look previous threads but didn't notice that one! ...
written 4.2 years ago by Jokhe120
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CNA clonality for non-WES/WGS data
... Does anyone know any tools to detect copynumber variations (CNA) from matched tumor-normal sequencing data. There are tools like Battenberg and TitanCNA but they are intended to be used with WGS/WES data. My data, in turn, is a targeted sequencing data of 40 cancer genes. At least for Titan CNA my d ...
clonality copynumber written 4.2 years ago by Jokhe120
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How to summarize variant data in multiple VCF files?
... I have analyzed normal-tumor samples with VarScan2 and now I have annotated variant data in VCF format; ##fileformat=VCFv4.1 ##source=VarScan2 ... #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR chr1 27107650 . TA T . PASS DP=543;SS=1;SSC=3;GPV=1.5919E-53;SPV=4.6338E ...
vcf varscan2 summary comut visualization written 4.2 years ago by Jokhe120 • updated 13 months ago by lincoln.harris0
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Comment: C: indel preprocessing prior to bam-readcount
... Thank you for your answer. The example case I am presenting in this post contains only deletions so it is very likely that this is caused by the bug you indicated. However, I have similar problem with all of my samples and some of them do contain also insertions. Insertions are also filtered out due ...
written 4.3 years ago by Jokhe120
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Answer: A: Coverage analysis in a targeted amplicon-based next-generation sequencing panel
... Bedtools is a good option indeed. I can also recommend Picard Tool's [CalculateHsMetrics][1] tool which is very useful when analyzing the success of targeted NGS sequencing. It doesn't give the result you are exactly asking for but it reports the percentage of bases covered less than nX times in tar ...
written 4.3 years ago by Jokhe120

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