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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
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vcf input but prompted me bcf parsing error #296

Closed shannjiang closed 5 years ago

shannjiang commented 5 years ago

Hi,

I am using denovogear to do dnm calling. My command is as follow:

dng dnm auto --ped 35-02451_trio1.ped --vcf 35-02451_trio1_filtered_v1.vcf --output_vcf 35-02451_trio1_filtered_v1_dngout.vcf

Attached please find my .vcf and .ped files.

My command prompted me such error info: DeNovoGear v1.1.1

output vcf file: 35-02451_trio1_filtered_v1_dngout.vcf Created SNP lookup table First mrate: 1 last: 1 First code: 6 last: 6 First target string: AA/AA/AA last: TT/TT/TT First tref: 0.0002388 last: 0.99301

Created indel lookup table First code: 6 last: 6 First target string: RR/RR/RR last: DD/DD/DD First prior: 0.05 last: 0.114

Created paired lookup table First target string: AA/AA last: TT/TT First prior 1 last: 1

BCF PARSING ERROR - Trios! -6 Exiting !

But I didn't provide .bcf file as input. How's this happened?

dng_input.zip

reedacartwright commented 5 years ago

Please try the develop branch and let us know if the error message still occurs.

shannjiang commented 5 years ago

But what's the flag for output vcf file in denovogear develop version? --output_vcf is not usable in the develop version. I checked its usage but didn't find the option: Usage: Autosomes: dng dnm auto --bcf bcf_f --ped ped_f [OR] dng dnm auto --vcf vcf_f --ped ped_f X chromosome in male offspring: dng dnm XS --bcf bcf_f --ped ped_f [OR] dng dnm XS --vcf vcf_f --ped ped_f X chromosome in female offspring: dng dnm XD --bcf bcf_f --ped ped_f [OR] dng dnm XD --vcf vcf_f --ped ped_f

Allowed Options: -p [ --ped ] arg Ped file to describe relationship between the samples -b [ --bcf ] arg BCF file, contains per-sample read depths and genotype likelihoods -v [ --vcf ] arg VCF file, contains per-sample read depths and genotype likelihoods -s [ --snp_mrate ] arg (=1e-8) Mutation rate prior for SNPs -i [ --indel_mrate ] arg (=1e-9) Mutation rate prior for INDELs -P [ --pair_mrate ] arg (=1e-9) Mutation rate prior for paired sample analysis -i [ --indel_mu_scale ] arg (=1.0) Scaling factor for indel mutation rate -c [ --pp_cutoff ] arg (=0.0001) Posterior probability threshold -R [ --rd_cutoff ] arg (=10) Read depth filter, sites where either one of the sample have read depth less than this threshold are filtered out -r [ --region ] arg Region of the BCF file to perform denovo calling. [string of the form "chr:start-end" -o [ --poly_rate ] arg (=1e-3) Polymorphsim rate - used in prior calculations -m [ --mu_scale ] arg (=1.0) Scaling factor for indel priors -w [ --write ] arg Write output to vcf file. --version display version information --help display usage informaiton --arg-file arg read command-line arguments from a file

reedacartwright commented 5 years ago

It's towards the bottom.

-w [ --write ] arg Write output to vcf file.
shannjiang commented 5 years ago

reedacartwright, thanks so much for your help and I got my first dng result!!

But I am confused how to explain the result. Because it seems not all of the PP_DNM are high in the output file. The truth is most of the PP_DNM are close to 0. Should I still contain this portion of SNPs whose PP_DNM are close to 0 as DNM? Or I should consider those SNPs with PP_DNM more than 0.5 as DNM (because PP_DNM is greater than PP_NULL in such case)?

Attached please find my result vcf file.

fam35_02451_trio1_dngout.zip

reedacartwright commented 5 years ago

I unfortunately can't provide many tips on converting the output of dng dnm into biological insight. I don't have experience working directly with the statistics outputted by dng dnm. My experience in analyzing mutations has been with the output of dng call.

reedacartwright commented 5 years ago

Closing because your error message is fixed in the develop branch.