search

dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
Apache License 2.0
102 stars 39 forks source link

what is the call from combined vcf that has no caller info #3

Closed arkyl closed 6 years ago

arkyl commented 6 years ago

Hi, I run parliament2 on DNAnexus. I am wondering what the calls are, that has no caller info. E.g: chr1 819974 DEL00162134SUR N . PASS SUPP=1;AVGLEN=385;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=1;END=820359;STRANDS=+- GT:SP ./.:.

I suppose that each call is from a caller. so is the above call from a caller but the info of the caller was not provided because it was genotyped? Thanks much !

fritzsedlazeck commented 6 years ago

Hi, thanks for reaching out. Can you explain if this is a per sample call or merged over multiple samples. In addition I am wondering if you could post multiple entries or if this is a full line or just cut? Thanks Fritz

arkyl commented 6 years ago

Sorry, didn't see this. It's a one sample vcf. My question is more about the output format. I attach a two line example txt. One line has CALLER info: MANTA. The other line didn't have caller info. In that case, can we know the caller that makes the SV call? Thanks much.

example.txt

slzarate commented 6 years ago

Hi, are you running SVTyper to generate the VCF file?

arkyl commented 6 years ago

Hi Samantha, Thanks for the reply. I used the parliament2 pipeline, which I believe used SVTyper.

I think I can now understand the output better. There is a *combined.genotyped.vcf file. In this file, there is SUPP info, e.g:

SUPP=3;, but there is no info about which 3 callers support the call.

I think the naive SURVIVOR output would have this info.

Thanks.

Yue

On Tue, Jul 17, 2018 at 1:43 PM, Samantha Zarate notifications@github.com wrote:

Hi, are you running SVTyper to generate the VCF file?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dnanexus/parliament2/issues/3#issuecomment-405667021, or mute the thread https://github.com/notifications/unsubscribe-auth/AAqSiuSnxTA9GkG66YIY6QlRBtuzoB8Yks5uHiJcgaJpZM4Utt7W .

fritzsedlazeck commented 6 years ago

Hi Yue, There are other flags in the INFO field that show that. Ultimately you can check these in the genotype caller columns subsequent of column 9 (I think).

thanks Fritz

arkyl commented 6 years ago

Hi Fritz, When there is SUPP=3, there are usually only two callers info provided. For example,

chr1 5414152 DEL00139798SUR N . PASS SUPP=3;AVGLEN=75.3333;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=1;END=5414227;STRANDS=+-;CALLERS=MANTA,DELLY GT:SP 0/1:MANTA,DELLY

Also, for the ones that were not genotyped, the caller info was not available.

It seems the available caller info in the *combined.genotyped.vcf are only the callers that were used for genotyping, but not the callers generated by parliament2 to actually support the SV. Thanks much.

Yue

On Tue, Jul 17, 2018 at 3:05 PM, Fritz Sedlazeck notifications@github.com wrote:

Hi Yue, There are other flags in the INFO field that show that. Ultimately you can check these in the genotype caller columns subsequent of column 9 (I think).

thanks Fritz

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/dnanexus/parliament2/issues/3#issuecomment-405693225, or mute the thread https://github.com/notifications/unsubscribe-auth/AAqSirimV0FYY2IUuEyo9-G5dMli3WKaks5uHjV1gaJpZM4Utt7W .

fritzsedlazeck commented 6 years ago

Mhm yeah, because CALLERS=MANTA,DELLY is not a SURVIVOR output. Thx Fritz

slzarate commented 6 years ago

Hi, this is a known bug with the version of SVTyper in this image. Within the next day or so I will be putting out a new release, and this should resolve your error. Stay tuned.

slzarate commented 6 years ago

@arkyl Hi, I believe this has been resolved by #10. Please download the 0.1.7 release and see if it works for you.

arkyl commented 6 years ago

Hi Samantha, I run the parliament2 0.1.7 on DNAnexus. I think the combined vcf still didn't have the call info for the ones that were not genotyped, i.e., the SP field in GT:SP is probably from SVtyper, not from SURVIVOR. When the call was not genotyped, the support SV caller info was lost. Thanks.

e.g:

when a call was not genotyped

chr1 921340 INV0076397SUR N . PASS SUPP=1;AVGLEN=103;SVTYPE=INV;SVMETHOD=SURVIVORv2;CHR2=1;END=921443;STRANDS=++ GT:SP ./.:.

when SUPP=3; but there is only one caller info

chr1 1350001 DEL0075681SUR N . PASS SUPP=3;AVGLEN=1365;SVTYPE=DEL;SVMETHOD=SURVIVORv2;CHR2=1;END=1351400;STRANDS=+-;CALLERS=CNVNATOR GT:SP 1/1:CNVNATOR

Yue

On Thu, Jul 19, 2018 at 12:30 PM, Samantha Zarate notifications@github.com wrote:

@arkyl https://github.com/arkyl Hi, I believe this has been resolved by

12 https://github.com/dnanexus/parliament2/pull/12. Please download

the 0.1.7 release and see if it works for you.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dnanexus/parliament2/issues/3#issuecomment-406337667, or mute the thread https://github.com/notifications/unsubscribe-auth/AAqSinEbwc1twS4VFgQQiRtbyyFv9yVgks5uILQxgaJpZM4Utt7W .

slzarate commented 6 years ago

Hi Yue,

OK, so I have looked into this and this is a feature, not a bug. What this means is that a caller has found something, but it hasn't been orthogonally verified, so use that call at your own risk. As a result, we will not be resolving this, but thanks for bringing it to my attention!

Samantha