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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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Port FastaAlternateReferenceMaker to GATK4 #4891

Closed chandrans closed 5 years ago

chandrans commented 6 years ago

@chandrans commented on Wed Jan 17 2018

Is FastaAlternateReferenceMaker going to be in GATK4? I did not see any mention of it. I hope other users will request it if there is demand.

User Report

Where is the fastaalternatereferencemaker in GATK4.0? I want to build a reference with mutation by fastaalternatereferencemaker, but I can not find the commond of fastaalternatereferencemaker , please tell me where ? Thank you !

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chandrans commented 6 years ago

9 people have requested this. I realize this is still low priority, but any chance someone would be willing to take this on?

Genetics2-tokyo commented 6 years ago

Hi Where is the fastaalternatereferencemaker in GATK4.0?

AidanQuinn commented 6 years ago

It's a very useful tool, would be great to have included in GATK4!

ryfa5051 commented 6 years ago

Would love to have this in GATK4, hopefully with an option for keeping the fasta headers to the name after the whitespace and not the default 1, 2, 3, etc. This would make it ideal for moving that data to Sequencher or any other assembly by name program.

EvoMedLab commented 6 years ago

This is an essential tool for people examining regions with both variant and invariant sites - basically anyone studying evolution. Please add this to 4.0.

davidecarlson commented 6 years ago

I would love to have this in GATK4 as well!

TepoltC commented 6 years ago

I'd also love to see this feature in v4 - as has been stated above, it's a great tool for a lot of evolutionary work.

ghost commented 6 years ago

This would be amazing to have in GATK 4. Super useful!

lbi-usp commented 6 years ago

Count me as another who would like to have it on GATK 4

avneeshbt commented 5 years ago

Please count me also. It is very useful tool. My whole pipeline is with GATK4, so it would be best to have this tool too.

rvosa commented 5 years ago

I would also like to have this, thanks.

migrau commented 5 years ago

+1

kescull commented 5 years ago

I'd also like to see this tool in GATK4. I'm just starting out in the area, but I think it will be useful for our proteogenomics-based work.

leoqiang commented 5 years ago

I would also like to have it in GATK4.

lbergelson commented 5 years ago

Due to popular demand we are going to port this in the near future.

ryfa5051 commented 5 years ago

How soon is the near future?

droazen commented 5 years ago

@ryfa5051 It's scheduled to be ported this quarter (so, either this month or next month).