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brentp / slivar

genetic variant expressions, annotation, and filtering for great good.
MIT License
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Data driven cutoffs #98

Closed Madelinehazel closed 3 years ago

Madelinehazel commented 3 years ago

Hi Brent,

Thanks for this excellent tool! Is it possible to explore data driven cutoffs for SVs? I'm trying to look at some info and format fields for SVs called by Manta in a trio using the following command:

slivar ddc \ --chrom "chr15" \ --info-fields 'MATE_BND_DEPTH,BND_DEPTH' \ --fmt-fields 'SR,PR' $vcf $ped

However, I get the following output from slivar, and the html file was not populated: slivar version: 0.1.11 5d6a5990fc06b52cbb1930806d03f786cf27d267 [slivar] wrote output to:slivar-ddc.html number of infos:0 trio:0

So the info fields, and the trio structure, don't seem to be picked up. I also tried the following command using the GATK Haplotype caller SNVs and indel vcf for the same trio:

slivar ddc \ --chrom "chr15" \ --info-fields 'MQ,DP,FS' \ --fmt-fields 'GQ' $vcf $ped

and similarly had the following output: > slivar version: 0.1.11 5d6a5990fc06b52cbb1930806d03f786cf27d267 [slivar] wrote output to:slivar-ddc.html number of infos:0 trio:0

Would appreciate your insight on the issue! Thanks, Madeline.

brentp commented 3 years ago

Hi, this looks like you don't have the trios specified correctly in your pedigree file. Can you show a full trio output in your $ped? Also, are you sure you have chr15 and not 15?

Madelinehazel commented 3 years ago

Thanks for the quick reply! The ped looks like this:

1159R 1159R_CH0531 1159R_CH0880 1159R_CH0879 2 2 1159R 1159R_CH0879 0 0 2 -9 1159R 1159R_CH0880 0 0 1 -9

I did try both 15 and chr15, and neither seemed to work unfortunately!

brentp commented 3 years ago

you have a very old version of slivar, try to update to v0.2.5, then if it's still broken, let's debug further.

Madelinehazel commented 3 years ago

Ahh of course, thanks! Working now.

brentp commented 3 years ago

glad to hear it.