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Search: Posts Made By: lgmSeq
Forum: Bioinformatics 10-29-2018, 06:24 AM
Replies: 6
Views: 9,916
Posted By lgmSeq
To filter out specific regions from a BAM file,...

To filter out specific regions from a BAM file, you could use the -U option of samtools view:

samtools view -b -L specificRegions.bed -U myFileWithoutSpecificRegions.bam myFile.bam >...
Forum: Bioinformatics 07-09-2018, 11:37 PM
Replies: 1
Views: 1,069
Posted By lgmSeq
CNV/SV merging: To merge/combine the common CNV...

CNV/SV merging:
To merge/combine the common CNV detected by your different callers, I would consider CNV that share a 70% reciprocal overlap measured by length and position (> 70% shared length) (as...
Forum: Bioinformatics 07-09-2018, 11:31 PM
Replies: 2
Views: 1,998
Posted By lgmSeq
CNV / SV detection and annotation

CNV/SV detection:
I suggest using different CNV callers: Control-freec, Lumpy, ERDS, BreakDancer
I advise then to merge the common CNV detected by your different callers. For that, I would consider...
Forum: Bioinformatics 07-09-2018, 11:20 PM
Replies: 1
Views: 841
Posted By lgmSeq
AnnotSV: An integrated tool for Structural Variations (SV) annotation

I suggest using AnnotSV (http://www.lbgi.fr/AnnotSV/) for SV/CNV annotation (with OMIM, DGV, 1000g, haploinsufficiency, TAD, ... and also with your own in-house information).

You can look at the...
Forum: Bioinformatics 07-09-2018, 09:36 AM
Replies: 3
Views: 1,304
Posted By lgmSeq
AnnotSV: An integrated tool for Structural Variations annotation

Hi,

I'm annotating my CNV/SV human events with the AnnotSV (http://www.lbgi.fr/AnnotSV/) tool.
PMID: 29669011 DOI: 10.1093/bioinformatics/bty304

It associates a complete panel of...
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