User: pegeot.henri
pegeot.henri • 0
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Posts by pegeot.henri
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... Hello,
I would like to know if any of you know why the **target mean coverage** is so different when calculated by Picard or Qualimap.
For thesame bam and bed files :
Exome A ; Qualimap = 127.8 ; Picard = 88.2
Exome B ; Qualimap = 151.9 ; Picard = 104.9
Exome A ; Qualimap = 113.6 ; Picard = 77. ...
written 2 days ago by
pegeot.henri • 0
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... > Doesn't Picard HS also output median coverage ?
Yes and it is different from qualimap and I have no idea why, for the same data:
Qualimap median coverage = 110X ; Picard Median coverage = 80X
I know picard does not consider duplicated read, I cannot find out if Qualimap does it...
Thank you, ...
written 6 days ago by
pegeot.henri • 0
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... Hello there, so I am analyzing metrics from two kit of exome sequencing and I have the following:
For 100M reads for both exome:
**Qualimap: median coverage:**
- Exome A = 150X
- Exome B = 110X
**Picard HS Metrics mean target coverage:**
- Exome A = 75X
- Exome B = 85X
How do you interpret th ...
written 6 days ago by
pegeot.henri • 0
• updated
6 days ago by
trausch • 1.2k
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... So I have done the following :
- Using `bedtool nuc` I have calculated the GC content of each region of my bed file
- Using samtools bedcov, I have calculated the average depth of coverage for each region of my bed :
`samtools bedcov -Q 30 Intervals.bed sample.bam | sort -k1,1 -k2,2n -k3,3n | awk ...
written 6 days ago by
pegeot.henri • 0
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... Is CollectGcBiasMetrics (Picard) what I am looking for ?
...
written 7 days ago by
pegeot.henri • 0
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... Hi,
I wonder what should I do to obtain a dataset to draw a plot showing GC content against mean depth for exome data (like [this][1]).
I have bam files, bed files, fastQ files but I don't even know where I should start.
Thanks
[1]: https://www.researchgate.net/figure/Normalized-depth-of-covera ...
written 7 days ago by
pegeot.henri • 0
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... To give more context I work in an hospital and I am looking for the most performant sequencing kit. This will lead to the choice of a technology for routine use for patients analysis. One of the key metrics I want to investigate is the target coverage efficiency for the same sequencing effort.
Conc ...
written 7 months ago by
pegeot.henri • 0
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... I am interested in comparing standard QC metrics. Amongst other things, I am particularly interested in the target Coverage efficiency as a function of number of reads. Downsampling is usually done in such cases as it allows a comparaison with the same amount of sequencing.
...
written 7 months ago by
pegeot.henri • 0
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... Hello,
I am performing exome comparisons between different technologies and different sequencing conditions.
I have downsampled my dataset for a fair comparison at 5M 10M ..... 60M (M = million of reads).
Amongst other things, I compare notably exomes with 2 x 150 bp vs 2 x 75 bp. But in both case ...
written 7 months ago by
pegeot.henri • 0
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... Hello again,
I have made some progress to filter vcf based on allelic balance. I used the tools vcffilterjdk with the following command line :
java -jar vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->G.hasAD()).map(G->G.getAD()).allMatch(A->A.length>1 &&am ...
written 7 months ago by
pegeot.henri • 0
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