User: Jokhe
Jokhe • 120
- 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 >
0
votes
0
answers
7.1k
views
0
answers
... Thank you Matt! Works like a charm! ...
written 3.5 years ago by
Jokhe • 120
7
votes
0
answers
7.1k
views
8 follow
0
answers
... 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 ...
written 3.5 years ago by
Jokhe • 120
• updated
14 months ago by
schroder.julia • 0
0
votes
0
answers
3.9k
views
0
answers
... 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
Jokhe • 120
8
votes
0
answers
3.9k
views
8 follow
0
answers
... 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 ...
written 3.6 years ago by
Jokhe • 120
0
votes
1
answer
2.0k
views
1
answer
... 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 ...
0
votes
1
answer
1.5k
views
1
answers
... Thank you! I tried to look previous threads but didn't notice that one! ...
written 4.2 years ago by
Jokhe • 120
2
votes
1
answer
1.5k
views
1
answer
... 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 ...
written 4.2 years ago by
Jokhe • 120
4
votes
2
answers
1.9k
views
2
answers
... 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 ...
written 4.2 years ago by
Jokhe • 120
• updated
13 months ago by
lincoln.harris • 0
0
votes
1
answer
2.7k
views
1
answers
... 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
Jokhe • 120
2
votes
3
answers
3.4k
views
3
answers
... 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
Jokhe • 120
Latest awards to Jokhe
No awards yet. Soon to come :-)
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1140 users visited in the last hour