Using priors with lumpy/lumpyexpress

[bharatij]

Hi,
I am using Lumpy to find structural variants. While reading paper I came across using 1000 genome SVs as a priors to use with Lumpy. I was trying to understand more about how to use priors with lumpy/lumpyexpress in the Lumpy documentation but so far I am not able to figure it out.
Can you please shed more light on it?
Thanks.

[ryanlayer]

Sure. To use priors you need to convert the regions that you want to "seed"
the analysis to BEDPE format, then simply include those files using the
lumpy -B option. Unfortunately lumpyexpress does not support this option,
so you will need to use lumpy directly.

On Thu, Jul 21, 2016 at 11:32 AM, bharatij notifications@github.com wrote:

Hi,
I am using Lumpy to find structural variants. While reading paper I came
across using 1000 genome SVs as a priors to use with Lumpy. I was trying to
understand more about how to use priors with lumpy/lumpyexpress in the
Lumpy documentation but so far I am not able to figure it out.
Can you please shed more light on it?
Thanks.

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Ryan Layer

[bharatij]

Thanks for the details. So if I have use deletion and duplication from 1000 genome project as a prior, I can make bedpe file from vcf using lumpy-sv/scripts/vcfToBedpe file and use the bedpe as a prior with lumpy. I was checking the the -B parameter you mentioned to include prior file but the documentation says it is output file parameter. Is it -bedpe parameter instead?
Please correct me if anything is wrong.
Once again, I appreciate your help.

[ryanlayer]

Unfortunately, vcfToBedpe is not going to help here. The format of the
BEDPE is:

1 1 101 1 9900 10100 1 9999 + + TYPE:DELETION

that last TYPE tag is very important since lumpy needs that to properly
cluster this breakpoint with the alignment. How to get your VCF into this
format depends on the fields you have available. If you have "END" in your
info field you can use something like:

bcftools query -f "%CHROM\t%POS\t%INFO/CIPOS\t%INFO/END\t%INFO/CIEND\n"
you.vcf.gz

to get the field, then trasform those fields with awk, python, etc.

On Thu, Jul 21, 2016 at 1:22 PM, bharatij notifications@github.com wrote:

Thanks for the details. So if I have use deletion and duplication from
1000 genome project as a prior, I can make bedpe file from vcf using
lumpy-sv/scripts/vcfToBedpe file and use the bedpe as a prior with lumpy. I
was checking the the -B parameter you mentioned to include prior file but
the documentation says it is output file parameter. Is it -bedpe parameter
instead?
Please correct me if anything is wrong.
Once again, I appreciate your help.

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