User: elcortegano

gravatar for elcortegano
elcortegano10
Reputation:
10
Status:
New User
Location:
Last seen:
3 days, 23 hours ago
Joined:
2 months, 3 weeks ago
Email:
e****************@ed.ac.uk

Posts by elcortegano

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
64
views
0
answers
Calling TE sequences from VCF files
... 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 ...
sniffles next-gen variant_calling written 6 days ago by elcortegano10
0
votes
0
answers
75
views
0
answers
What does "Infinity" QUAL values mean in VCF files
... 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 ...
vcf next-gen written 4 weeks ago by elcortegano10
0
votes
1
answer
171
views
1
answers
Comment: C: Are reads with the same length and position always "duplicates"
... 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 elcortegano10
0
votes
1
answer
171
views
1
answers
Comment: C: Are reads with the same length and position always "duplicates"
... 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 elcortegano10
0
votes
1
answer
171
views
1
answers
Comment: C: Are reads with the same length and position always "duplicates"
... 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 elcortegano10
0
votes
1
answer
171
views
1
answers
Comment: C: Are reads with the same length and position always "duplicates"
... Thank you, I will try that ...
written 7 weeks ago by elcortegano10
0
votes
1
answer
171
views
1
answers
Comment: C: Are reads with the same length and position always "duplicates"
... yes, thank you for noticing, I will update the post ...
written 7 weeks ago by elcortegano10
6
votes
1
answer
171
views
5 follow
1
answer
Are reads with the same length and position always "duplicates"
... 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 ...
next-gen picard written 7 weeks ago by elcortegano10
0
votes
2
answers
179
views
2
answers
Comment: C: Is it possible to run IGV in batch mode without opening the GUI?
... `xvfb-run --auto-servernum igv.sh -b script.bat` worked for my, thank you!! ...
written 8 weeks ago by elcortegano10
3
votes
2
answers
179
views
2
answers
Is it possible to run IGV in batch mode without opening the GUI?
... 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. ...
next-gen alignment igv written 8 weeks ago by elcortegano10 • updated 8 weeks ago by steve2.4k

Latest awards to elcortegano

Scholar 9 weeks ago, created an answer that has been accepted. For A: How to run Picard docker image

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 883 users visited in the last hour