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  • 20:24
    StephenHwang closed #3666
  • 20:24
    StephenHwang commented #3666
  • May 21 02:19
    adamnovak commented on 26f49a7
  • May 21 00:56

    adamnovak on long_read_giraffe_select_minimizers

    Apply suggestions from code rev… (compare)

  • May 21 00:56
    adamnovak synchronize #3665
  • May 21 00:35
    adamnovak commented #3666
  • May 20 20:58
    adamnovak commented on 86bd3ff
  • May 20 20:48
    StephenHwang opened #3666
  • May 20 20:36
    adamnovak commented on ded8e2f
  • May 20 19:23
    StephenHwang opened #3665
  • May 20 19:19

    StephenHwang on long_read_giraffe_select_minimizers

    Rename variable for number of s… (compare)

  • May 20 19:13

    StephenHwang on long_read_giraffe_select_minimizers

    Enable capping number of minimi… (compare)

  • May 20 15:18
    lsoldini commented #3664
  • May 20 15:08
    jeizenga commented #3664
  • May 20 14:46
    lsoldini commented #3664
  • May 20 10:57
    lsoldini commented #3653
  • May 19 21:01
    adamnovak commented on 2ab8987
  • May 19 19:58
    lsoldini commented #3664
  • May 19 19:47
    jeizenga closed #3664
  • May 19 19:47
    jeizenga commented #3664
JervenBolleman
@JervenBolleman
Ok, it is quite simple your kernel really is too old!
deliciouslytyped
@deliciouslytyped:matrix.org
[m]
:'D
im curious what syscall its choking on
JervenBolleman
@JervenBolleman
You are on a cent-os/redhat/oracle-linux 6
deliciouslytyped
@deliciouslytyped:matrix.org
[m]
oh actually it should be enough to run strace
JervenBolleman
@JervenBolleman
That is no longer a supported system
hgz2021
@hgz2021
alas
I don't have root permission
so difficult
JervenBolleman
@JervenBolleman
Then tell the person who does have root permission that they are running a not updated system that has known security issues
That this needs to be fixed
I would suggest compiling vg yourself but that is not going to work on a cent-os 6 box either
hgz2021
@hgz2021
I see. Thank you for your help
JervenBolleman
@JervenBolleman
Sorry to be the bringer of bad news
hgz2021
@hgz2021
Bad news is better than no news
deliciouslytyped
@deliciouslytyped:matrix.org
[m]
@adamnovak: I didnt forget about this ive just been elbow deep in other stuff, I plan to get back to it eventually
Groza Cristian
@cgroza
Hi, is there a way to get a FASTA file of haplotypes, given a genome graph and a gbwt.
hgz2021
@hgz2021
Hi, I have a problem here.
I now combine the VCF files of multiple varieties that store SV together to build vg. Then run "Index", "Map", "Pack", "Call". A few varieties came out.
But for other varieties, the file at the "call" step comes out empty
@cgroza
@deliciouslytyped:matrix.org
And there are no runtime errors
deliciouslytyped
@deliciouslytyped:matrix.org
[m]
(I don't know anything about actually using vg sorry :) )
hgz2021
@hgz2021
What requirements does VG have for input fastQ files?
hgz2021
@hgz2021
My input file fastA /fastq is quite large, can I split it into multiple input files during the map step? Then combine the generated GAM files? Vg and the corresponding command? Or you can just use "cat"?
@ryan-williams
@mlin
@adamnovak
Adam Novak
@adamnovak
@hgz2021 vg can take most FASTQ files, I think. They have to actually be conformant FASTQ, and the quality string length has to match the sequence length. All the reads are supposed to have unique names.
I don't actually remember what FASTQ offset we assume; it should be the same as what BWA uses.
If you're using paired FASTQ we assume one fragment length distribution for the whole file.
As for splitting the FASTQ and combining the GAMs, you can definitely do that. GAM files can be safely concatenated with cat.
I'm not sure why you would be getting empty VCFs at the end of some vg pipelines; I think you'd have to do QC back along the pipeline. Are the read alignments you get out of the mapping step reasonable when you e.g. vg stats -a whatever.gam?
Adam Novak
@adamnovak
If you think you've found a bug, you can report it on the vg github with the files needed to reproduce it, and we can see if we can work out what is broken.
hgz2021
@hgz2021
@adamnovak Thank you very much,Now I have another question, I want to put my previous "cat" together with gAM, I want to know its mapping rate. Can VG do this for me?
hgz2021
@hgz2021
@kiwiroy
hgz2021
@hgz2021
I was thinking about converting GAM to BAM,but "surject", there was a problem. I didn't make it. As for surject-to BAM in "Map". It takes too long for me.
Adam Novak
@adamnovak
@hgz2021 Do you mean speed or fraction mapped? vg map --log-time should do speed. And vg stats -a will count how many alignments are actually aligned somewhere, from a GAM.
hgz2021
@hgz2021
Thank you for your help. My problem is solved.
Groza Cristian
@cgroza
Hi, how do I calculate read support with vg pack and a graph (gbz) created by vg autoindex in the giraffe workflow?
They don't seem to accept this graph format, and I am trying to genotype some structural variants.
Groza Cristian
@cgroza
I also notice vg call does not accept gbz. How do I input the giraffe alignments into vg call then?
Thank you in advance, and any clues are greatly appreciated.
Groza Cristian
@cgroza
I have tried converting to XG format and working that way, but the vg call output is empty.
Narendra Meena
@narendrameena
fatal error: google/protobuf/port_def.inc: No such file or directory
10 | #include <google/protobuf/port_def.inc>
| ^~~~~~~~~~
I am getting this error when instaling latest version of VG on ubuntu 20.04. please anybody can suggest how can I resolve this error ?
hgz2021
@hgz2021
image.png
Hello, I've been using the giraffe recently, and in vg autoindex, two of the two files are the fa and the vcf.gz file. I see these two files in vg/test/wiki-data/mock-hs37d5/data/ this directory. What do I want to know about the vcf.gz file? What is the role of the giraffe? And can the process of assembly to the genome level fa file be an input?
hgz2021
@hgz2021
The above picture is the content of the.vcf. Gz file you provided for the test
abanerjee10
@abanerjee10
Hi, how do I do semiglobal alignment with vg? I have only found local and banded global alignment
hgz2021
@hgz2021
Hello, I am engaged in group research. My question is that I want to get GVCF in the result of VG call, but I have not found this parameter, which is very important for my next research.