User: finswimmer

gravatar for finswimmer
finswimmer600
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600
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Germany
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4 hours ago
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8 months, 3 weeks ago
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Posts by finswimmer

<prev • 117 results • page 1 of 12 • next >
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Answer: A: CollectHsMetrics Mean_Target_Coverage vs. mean_coverage in PER_TARGET_COVERAGE
... Argh, it's all about mathematic. I've forget to include the length of the target regions. Of course the mean coverage over all target regions is sum(mean_target_coverage * length)/sum(length of all target region). fin swimmer ...
written 1 day ago by finswimmer600
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CollectHsMetrics Mean_Target_Coverage vs. mean_coverage in PER_TARGET_COVERAGE
... Hello, again a question to picard's CollectHsMetrics. I run it with the parameter PER_TARGET_COVERAGE. I would expect that the mean target coverage reported in the HsMetrics file is the same, as the average of all mean coverages reported in the target coverage file. But in my cases the value in th ...
picard collecthsmetrics written 2 days ago by finswimmer600
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Answer: A: dbsnp hg 38
... Hello, I cannot say whether this is a copy of the correct file. I would go to the [download page][1] of dbsnp. For human you find the current version [here][2]. fin swimmer [1]: ftp://ftp.ncbi.nih.gov/snp/ [2]: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh38p7/VCF/All_20170710.vc ...
written 14 days ago by finswimmer600
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Answer: A: Big differences with CollectHsMetrics
... Finally I could solve it. The problem was how I use MarkDuplicates and how MarkDuplicates work. I run it on the combined bam file which contain the single end merged read and the paired end reads that could not be merged. MarkDuplicate consider only about the 5' mapping positition. The mixture of ...
written 15 days ago by finswimmer600
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Comment: C: Paired-end amplicon sequencing data
... > So, should I use both sequences/possibilities separately although the belong to the same read? Again, it may depend on what is your goal. Variant Calling? A variant caller should consider that these reads are a pair and vote it in some way that there is a mismatch between them. Or the way I pr ...
written 18 days ago by finswimmer600
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Answer: A: What is " ./.:. " in the GT output of VCF/BCF
... Hello, the first column in the vcf describe the chromosom on which the variant is located. "1" and "GL000208.1" are not the same. "1" is chromosom 1 and "GL000208.1" seems to be an alternate scaffold that couldn't be mapped to a chromosome. So the merging result is correct. You just have in one sa ...
written 18 days ago by finswimmer600
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Comment: C: Help in writing NGS pipeline (or: the road from fasta to vcf)
... > You need to do a base recalibration before SNP calling. It depends... Have a look in the [discussion][1] we had here some days ago. [1]: https://www.biostars.org/p/280274/ ...
written 18 days ago by finswimmer600
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Comment: C: Major challenges of aligning the NGS data
... Is this a homework ? ...
written 18 days ago by finswimmer600
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Answer: A: Big differences with CollectHsMetrics
... It seems that I have found at least some reasons for the big differences. At first, the version of picard tools I used was 2.9. The current version is 2.14. In the earlier version there was a bug handling overlapping paired reads. With the new version the differences in the coverage are now slightl ...
written 20 days ago by finswimmer600
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Comment: C: Big differences with CollectHsMetrics
... Sorry, i have forgot to mention it. I mapped both, the merged and unmerged reads and combined the bam files afterwards. fin swimmer ...
written 21 days ago by finswimmer600

Latest awards to finswimmer

Scholar 15 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Scholar 17 days ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Centurion 29 days ago, created 100 posts.
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Supporter 3 months ago, voted at least 25 times.
Scholar 4 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Student 4 months ago, asked a question with at least 3 up-votes. For Why not merging?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file
Scholar 5 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Commentator 7 months ago, created a comment with at least 3 up-votes. For A: sam file error
Scholar 8 months ago, created an answer that has been accepted. For A: How to merge multiple bam files into single bam file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: How to merge multiple bam files into single bam file

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