mergeCavemanResults

[ramaniak]

Hello,
I did not find any documentation for this script in the main documentation page, but did run across it when searching the repository. Is this script meant to be run after the estep to combine all the variant calls?

I did try running it as follows:

mergeCavemanResults --output cavemen_muts_all_merge.vcf -s splitList -f results/%/%.muts/vcf
and get the following error

Expected 1726 files but got 0. at ./mergeCavemanResults line 54.

Could you please let me know if this is meant to be run this way? If not, is there a tool you would recommend for combining the final variant calls?

thanks
Arun

[ramaniak]

Hello,
I am also seeing some strange calls as below where it is reporting the same ref and alt read at many locations.

10	126678241	.	G	G	.	.	DP=1132;MP=1.0e+00;GP=2.3e-30;TG=GG/GGGGG;TP=7.1e-04;SG=GG/AGGGG;SP=1.0e+00	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:2:162:0:0:4:129:0:9.8e-01	0|0:0:5:443:0:0:13:374:0:9.8e-01

[keiranmraine]

Hi Arun,

We'd recommend using the wrapper code to make your life easier and especially for your first run as it's easier to determine if issues are data rather than execution using this:

https://github.com/cancerit/cgpCaVEManWrapper

It can be run in a farm compatible manner.

Regards,
Keiran

[ramaniak]

Hi Keiran, Thanks, I will give that a try. Arun

…

On Tuesday, December 6, 2016, Keiran Raine ***@***.***> wrote: Hi Arun, We'd recommend using the wrapper code to make your life easier and especially for your first run as it's easier to determine if issues are data rather than execution using this: https://github.com/cancerit/cgpCaVEManWrapper It can be run in a farm compatible manner. Regards, Keiran — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#57 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFzoBm58aaPDncJggwminor__g0KgMeMks5rFS0OgaJpZM4LEnbk> .

[ramaniak]

Hello Keiran,
I am not sure if you would like me to continue this thread or start a new issue at cgpCaVEManWrapper. I can move it if that is preferable.

There are two flags that are stated as "required" for which I am not sure what the preferred input is:

1. -germline-indel
2. -unmatched-vcf

I am working with exomes and is there a particular caller you recommend for getting germline indels? Also, I am not sure what is expected under unmatched vcf and what it means by "Directory containing unmatched normal VCF files or http/ftp base". Is it possible to work without the indel call or unmatched-vcfs? I was not able to get much information from the documentation.

thanks
Arun

[ghost]

@ramaniak

1. -germline-indel Is a file produced by cgpPindel used in flagging the CaVEMan calls
2. -unmatched-vcf A vcf panel of unmatched normals (again used in flagging). A description of how to produce this file can be found in the upcoming Current Protocols in Bioinformatics paper (unfortunately not yet published).

For now you can avoid these by using the -no-flagging parameter and providing the following:

1. -germline-indel - A bed file containing the single false bed entry 1 0 1
2. -unmatched-vcf - Any directory

This has highlighted an issue with caveman.pl that when requesting no flagging, these files would still be required. I'll open an issue in cgpCaVEManWrapper to ensure this gets fixed.

Dave

[ramaniak]

Hello David, Thanks very much, those changes seem to be working. Any chance you would be able to share the just the part regarding the unmatched vcf from the paper prior to publication? Look forward to seeing the published version. thanks Arun

…

On Wed, Dec 7, 2016 at 2:27 PM, David Jones ***@***.***> wrote: @ramaniak <https://github.com/ramaniak> 1. -germline-indel Is a file produced by cgpPindel <https://github.com/cancerit/cgpPindel> used in flagging the CaVEMan calls 2. -unmatched-vcf A vcf panel of unmatched normals (again used in flagging). A description of how to produce this file can be found in the upcoming Current Protocols in Bioinformatics paper (unfortunately not yet published). For now you can avoid these by using the -no-flagging parameter and providing the following: 1. -germline-indel - A bed file containing the single false bed entry 1 0 1 2. -unmatched-vcf - Any directory This has highlighted an issue with caveman.pl that when requesting no flagging, these files would still be required. I'll open an issue in cgpCaVEManWrapper <https://github.com/cancerit/cgpCaVEManWrapper> to ensure this gets fixed. Dave — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#57 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFzoBuvZ_-aYdCSjriHuSr6rFPmi3fGYks5rFwiHgaJpZM4LEnbk> .

[ramaniak]

Hello,
The wrapper script runs through the whole pipeline and generates the merged muts and snps file as expected.

Unfortunately, I am seeing a few strange calls in the final vcf file.

10      115370307       e848aa14-bd83-11e6-9994-dbef58c5c9a6    C       C       .       .       DP=863;MP=1.0e+00;GP=2.9e-17;TG=CG/CC;TP=2.9e-17;SG=CC/CT;SP=1.0e+00    GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM   0|1:0:60:0:0:0:103:0:0:1.0e+00  0|0:2:221:14:0:1:430:32:0:9.3e-01

As you can see in the example above the ref and alt variants are both 'C'. This appears in a few of my samples and I was wondering if you knew why this might be occurring?

thanks
Arun

[keiranmraine]

Hi, just to follow up on your comment here. See point 1 here for an explanation.

There is a issue open for the correction of this #63