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walaj / svaba

Structural variation and indel detection by local assembly
GNU General Public License v3.0
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SvABA on 10X data #80

Closed mzwaig closed 4 years ago

mzwaig commented 4 years ago

Hi Jeremiah,

I ran SvABA on my 10X data, aligned using their barcode-aware aligner. I know SvABA is meant for standard WGS but it managed to pull out the barcode tags which support the SVs.

My question is does SvABA take into account the linked-read barcodes or is it a fluke that they are returned in the output.

Thanks, Melissa

walaj commented 4 years ago

Hi Melissa, It does track BX tags! It should report the number of supporting tags. I haven't extensively incorporated 10X capabilities into svaba, but this is something that it does track and report. (will close unless further issues). Best, Jeremiah

distilledchild commented 1 year ago

@mzwaig Hi, I am wondering which aligner did you use? I want to take the exact same steps for using svaba, but I am searching for aligner. I am not sure I can use longranger's output yet..! Thanks.

mzwaig commented 1 year ago

I used the LongRanger output/BAM

walaj commented 1 year ago

svaba has BWA-MEM baked into it, which it uses for re-realignment and contig-to-genome alignment.

svaba will also track 10X read support and report it in the genotype field. You may have to let it know you want this. If you do svaba run —help there should be an option for tracking BX tags.

On Thu, Dec 1, 2022 at 5:04 PM mzwaig @.***> wrote:

I used the LongRanger output/BAM

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distilledchild commented 1 year ago

@walaj @mzwaig Thank you so much for you all!

distilledchild commented 1 year ago

@walaj Hi, I have a few questions! firstly, the option tracking BX tags is --read-tracking Output options? And I am curious I can use gap file of my genome assembly for blacklist option.

Thank you so much for the great tool!

walaj commented 1 year ago

Reviewing the code again, the tracking of BX tags happens by default. You shouldn't have to add a flag, that was my mis-remembering how this was configured.

The --read-tracking will print out the QNAMES of all supporting reads, which greatly expands the size of the output files and mostly useful for targeted runs or debugging. It is a separate feature from BX tags.

The blacklist file is used to skip very repetitive areas where reads are aligned but unlikely to give a meaningful result (while also bogging down the caller). If there is a gap in the assembly, reads shouldn't be aligned there anyway so this wouldn't do much I believe. One strategy to make a blacklist file is to exclude areas with wildly high genome coverage, like 50x + the mean coverage -- these are often found at centromeres etc.

On Thu, Dec 1, 2022 at 5:44 PM a gopher @.***> wrote:

@walaj https://github.com/walaj Hi, I have a few questions! firstly, the option tracking BX tags is --read-tracking Output options? And I am curious I can use gap file of my genome assembly for blacklist option.

Thank you so much for the great tool!

— Reply to this email directly, view it on GitHub https://github.com/walaj/svaba/issues/80#issuecomment-1334540457, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUZ7CC2J7NA7CNNXA62T5DWLES3XANCNFSM4LDCLRHA . You are receiving this because you were mentioned.Message ID: @.***>

distilledchild commented 1 year ago

@walaj Thank you for your great advice and and the tool. I really appreciate your support and help!!