v0.2.0

v0.2.0

• skip non ACGT alts (@migbro #39)
• grab description from input vcf and propagate to annotated VCFs (@dmiller15, @migbro #34, #35)

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.2.0/echtvar \
    && chmod +x ~/bin/echtvar \
    && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

"." for missing floats

v0.1.9

• report missing float as . (thanks @dmiller15 #32)

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.9/echtvar \
    && chmod +x ~/bin/echtvar \
    && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

large files and other minor changes

v0.1.8

• better help message indicating how to output bcf/vcf.gz (thanks @dvg-p4)
• fix missing value in cadd example (thanks @dvg-p4)
• doc types (thanks @enormandeau)
• handle big files (#30)

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.8/echtvar \
    && chmod +x ~/bin/echtvar \
    && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

v0.1.7

changes

• add wiki page and more information about decomposing variants
• clarify warning on non ACGT (#23)
• better error messages on missing/bad zip file

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.7/echtvar \
    && chmod +x ~/bin/echtvar \
    && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

vcf-header + limit warnings

v0.1.6

• change VCF header (#19)
• output fewer warnings for '*' and other alternate alleles (#22 thanks @liserjrqlxue)

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.6/echtvar \
    && chmod +x ~/bin/echtvar \
   && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

osx and dbNSFP

v0.1.5

• fix build on OSX (#18 from @sstadick)
• handle empty alts (#16 from @sstadick)
• add script for converting dbNSFP -> VCF -> echtvar encode

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.5/echtvar \
    && chmod +x ~/bin/echtvar \
   && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

filter fix

v0.1.4

• fix bug with filter not removing (not filtering) variants correctly.

Get Started

To get started, download the static linux binary here, then chmod +x and execute:

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.4/echtvar \
    && chmod +x ~/bin/echtvar \
   && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

v0.1.3: don't use set_threads after reading header

This release fixes a major bug with dense variant files (like spliceAI)

v0.1.3

• exit with error on multi-allelics (previously, only first allele was used) ( #11)
• more docs on conf file (thanks @m-pauper)
• fix compression error for very dense regions (#12)
• major: fix error when using hts_set_threads more than once and after reading header (#12)

Get Started

To get started, either download the static linux binary here, then chmod +x and execute.

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.3/echtvar \
    && chmod +x ~/bin/echtvar \
   && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

bugfix

This release fixes a major bug (with a minor change) that rendered echtvar nearly unusable. The bug was related to string fields added in last release.

Get Started

To get started, either download the static linux binary here, then chmod +x and execute.

wget -O ~/bin/echtvar https://github.com/brentp/echtvar/releases/download/v0.1.2/echtvar \
    && chmod +x ~/bin/echtvar \
   && ~/bin/echtvar -h 

Experienced rust users can build with cargo
Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download

v0.1.1

This release adds the ability to annotate with multiple echtvar files and to annotate with string fields, including support for extracting the FILTER field. Here is the changelog:

v0.1.1

• support multiple echtvar files to echtvar anno. This makes it possible to annoate with, for example gnomad and dbsnp.
• support string fields. This works for fields with a lowish number (max of thousands) of unique values.
• support extracting FILTER field from annotation VCF. So now can annotate with, e.g. gnomad FILTER field via:

  {"field": "FILTER", "alias": "gnomad_filter"},
  

  in the json file for echtvar encode. "FILTER" is a special-case, all other fields are from the INFO.

⚠️ echtvar requires a precessor that supports SSE4.1 instructions. Using echtvar on an unsupported processor will result in a SIGILL.

Get Started

To get started, either download the static linux binary here, then chmod +x and execute; or use cargo build

Please let me know any (non SIGILL) issues with the binary. This is my first time distributing rust binaries.

Annotation files

you can create your own annotation files using echtvar encode. We provide a pre-made file for hg38 whole genomes from gnomad v3.1.2. It can be retrieved with:

curl -L -o gnomad.v3.1.2.echtvar.v2.zip https://surfdrive.surf.nl/files/index.php/s/nJPDxM3b9C7hkM2/download

The 7.1GB gnomad.v3.1.2.echtvar.v2.zip file is created using this example json

a smaller (2.5GB) file with only popmax AF is available with:

curl -L -o gnomad.v3.1.2.echtvar.popmax.v2.zip  https://surfdrive.surf.nl/files/index.php/s/LddbAYQAYPqtYu6/download