User: elcortegano
elcortegano • 10
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Posts by elcortegano
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... I have run the software [sniffles](https://github.com/fritzsedlazeck/Sniffles/wiki) to call structural variants from Pacbio sequences. In the resultant VCF file, most of entries in the ALT field look like:
N[chromosome_3:7199420[
In the example above, this is actually for a variant in a differ ...
written 6 days ago by
elcortegano • 10
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... I have a VCF file with a lot of "Infinity" values for the QUAL parameter in several invariant sites. Other invariant sites does not have these values, but rather numerical values.
I need to get a numeric value of QUAL, including for invariant sites, but cannot operate with these Inf values, special ...
written 4 weeks ago by
elcortegano • 10
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... The haplotypes were generated without that option, and the resultant gVCFs files were combined for calling variants with CombineGVCFs and GenotypeGVCFs. In that moment, I realized that some variants in the VCF (mostly indels) do not match the positions shown in IGV, when using the BAMs that were use ...
written 7 weeks ago by
elcortegano • 10
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... I have made an important edit in the post. I forgot to say that these "duplicates" are seen in the BAM files generated by HaplotypeCaller (which performs local realignments). In other files, MarkDuplicates seem to be more successful and I do not see these duplicates ...
written 7 weeks ago by
elcortegano • 10
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... Thank you for the reply, it helps me understand this is something might actually be happening. These "duplicates" typically have a length of 40bp in my dataset, but do not know exactly what is that expected insert size (I'm pretty new with this). Looking other reads, I'd say that these duplicates ar ...
written 7 weeks ago by
elcortegano • 10
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... Thank you, I will try that ...
written 7 weeks ago by
elcortegano • 10
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... yes, thank you for noticing, I will update the post ...
written 7 weeks ago by
elcortegano • 10
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5 follow
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... I'm struggling to understand that. I have some BAM files that have been processed with Picard tool MarkDuplicates, both using the REMOVE_DUPLICATES flag and not. In both cases, I can see in IGV some reads with the exactly same length, position, orientation and composition in bases. Why haven't been ...
written 7 weeks ago by
elcortegano • 10
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... `xvfb-run --auto-servernum igv.sh -b script.bat` worked for my, thank you!!
...
written 8 weeks ago by
elcortegano • 10
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... I'm running IGV in batch mode following the steps described in the [IGV website](https://software.broadinstitute.org/software/igv/batch).
When I enter a command like the following one in the terminal, IGV opens, runs as expected, and saves a snapshot. Everything OK.
bash igv.sh --batch=script. ...
written 8 weeks ago by
elcortegano • 10
• updated
8 weeks ago by
steve • 2.4k
Latest awards to elcortegano
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9 weeks ago,
created an answer that has been accepted.
For A: How to run Picard docker image
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